Package 'signifinder'

Title: Collection and implementation of public transcriptional cancer signatures
Description: signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.
Authors: Stefania Pirrotta [cre, aut] , Enrica Calura [aut]
Maintainer: Stefania Pirrotta <[email protected]>
License: AGPL-3
Version: 1.7.0
Built: 2024-07-02 03:54:13 UTC
Source: https://github.com/bioc/signifinder

Help Index

Adenosine Signaling Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

ADOSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr", ...)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
...

other arguments passed on to the gsvaParam function.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
ADOSign(dataset = ovse)

Antigen Processing Machinery Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

APMSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  author = "Wang",
  whichAssay = "norm_expr",
  hgReference = "hg38",
  ...
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".
...

other arguments passed on to the gsvaParam function.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
APMSign(dataset = ovse)

Adult Stem Cell Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

ASCSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
ASCSign(dataset = ovse)

Autophagy Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

autophagySign(
  dataset,
  nametype = "SYMBOL",
  author = "Xu",
  whichAssay = "norm_expr",
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
autophagySign(dataset = ovse)

Show Available Signatures

Description

It returns a table with all the information of the signatures collected in signifinder.

Usage

availableSignatures(
  tumor = NULL,
  tissue = NULL,
  topic = NULL,
  requiredInput = NULL,
  description = TRUE
)

Arguments

tumor

character vector saying the type of tumors for which signatures are developed. Used to filter the signatures in the table.
tissue

character vector saying the type of tissues for which signatures are developed. Used to filter the signatures in the table.
topic

character vector saying the signature topics. Used to filter the signatures in the table.
requiredInput

character string saying the type of data required in input by the signature. Either one of "microarray", "rnaseq" or "sc". Used to filter the signatures in the table.
description

logical. If TRUE it shows the signature's description.

Value

A data frame with 12 variables:

signature

name of the signature

scoreLabel

label of the signature when added inside colData section

functionName

name of the function to use to compute the signature

topic

main cancer topic of the signature

tumor

tumor type for which the signature was developed

tissue

tumor tissue for which the signature was developed

cellType

cell type for which the signature was developed

requiredInput

type of data with which the signature was developed

transformationStep

data transformation step performed inside the function starting from the user's 'normArray' or 'normCounts' data

author

first author of the work in which the signature is described

reference

reference of the work

description

signature description and how to evaluate its score

...

Examples

availableSignatures()

Breast Cancer Cellular States Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

breastStateSign(
  dataset,
  nametype = "SYMBOL",
  whichAssay = "norm_expr",
  isMalignant = NULL,
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
isMalignant

logical vector of the same length of ncol(dataset), where TRUE states malignant cells and FALSE states non-malignant cells.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)

Cell-cycle Signature classifier

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

cellCycleSign(
  dataset,
  nametype = "SYMBOL",
  author = "Lundberg",
  inputType = "microarray",
  whichAssay = "norm_expr"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
cellCycleSign(dataset = ovse, inputType = "rnaseq")

Chemokine Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

chemokineSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  whichAssay = "norm_expr"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
chemokineSign(dataset = ovse, inputType = "rnaseq")

Chromosomal instability Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

CINSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  whichAssay = "norm_expr"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
CINSign(dataset = ovse, inputType = "rnaseq")

CIS (carcinoma-in situ) Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

CISSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
CISSign(dataset = ovse)

EMT-Inflammation Combined Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

CombinedSign(
  dataset,
  nametype = "SYMBOL",
  whichAssay = "norm_expr",
  hgReference = "hg38",
  weighted = FALSE
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".
weighted

logical value, saying whether the score should be calculated with or without weights.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
CombinedSign(dataset = ovse)

ConsensusOV Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

consensusOVSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr", ...)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
...

optional parameters to be passed to get.subtypes.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
consensusOVSign(dataset = ovse)

Correlation Plot

Description

Given multiple signatures, the function plots signatures correlations.

Usage

correlationSignPlot(
  data,
  whichSign = NULL,
  sampleAnnot = NULL,
  selectByAnnot = NULL
)

Arguments

data

an object of type SummarizedExperiment. Output of the signatures functions.
whichSign

character vector saying the signatures to plot. If not specified, all the signatures inside data will be plotted. Other signatures not computed with signifinder can be added in the vector if they are also included in che colData section of data.
sampleAnnot

character vector containing samples' annotations.
selectByAnnot

character string saying the subgroup from 'sampleAnnot' used to compute the correlation plot.

Value

An object of class "openair".

Examples

data(ovse)
correlationSignPlot(data = ovse)

COX-2-associated Inflammatory Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

COXISSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
COXISSign(dataset = ovse)

DNA Repair Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

DNArepSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  whichAssay = "norm_expr"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
DNArepSign(dataset = ovse, inputType = "rnaseq")

Extracellular Matrix Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

ECMSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr", ...)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
...

other arguments passed on to the ssgseaParam function.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
ECMSign(dataset = ovse)

Epithelial-Mesenchymal Transition Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

EMTSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  author = "Miow",
  whichAssay = "norm_expr",
  hgReference = "hg38",
  ...
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".
...

other arguments passed on to the ssgseaParam function.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
EMTSign(dataset = ovse, inputType = "rnaseq")

Evaluation Plot

Description

A multipanel plot that shows: (i) a value of the goodness of a signature for the user's dataset. This is a combination of the parameters shown in the other pannels; (ii) the percentage of genes from the signature gene list that are actually available in the dataset; (iii) the percentage of zero values in the signature genes, for each sample; (iv) the correlation between signature scores and the sample total read counts; (v) the correlation between signature scores and the percentage of the sample total zero values.

Usage

evaluationSignPlot(
  data,
  nametype = "SYMBOL",
  whichSign = NULL,
  whichAssay = "norm_expr",
  sampleAnnot = NULL,
  selectByAnnot = NULL
)

Arguments

data

an object of type SummarizedExperiment. Output of the signatures functions.
nametype

character string saying the type of gene name ID (row names in data). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichSign

character vector saying the signatures to plot. These must be signatures computed with signifinder. If not specified, all the signatures inside data will be plotted.
whichAssay

integer scalar or string indicating which assay of data to use.
sampleAnnot

character vector containing samples' annotations.
selectByAnnot

character string saying the subgroup from 'sampleAnnot' used to compute the evaluation plot.

Value

A ggplot object.

Examples

data(ovse)
evaluationSignPlot(data = ovse)

ExpandedImmune Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

expandedImmuneSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
expandedImmuneSign(dataset = ovse)

Ferroptosis Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

ferroptosisSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "rnaseq",
  author = "Ye",
  whichAssay = "norm_expr",
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
ferroptosisSign(dataset = ovse)

Genes' Signatures' Heatmap

Description

Given one or multiple signatures, the function returns a heatmap of the expression values of the genes included in each of them.

Usage

geneHeatmapSignPlot(
  data,
  nametype = "SYMBOL",
  whichSign,
  logCount = FALSE,
  whichAssay = "norm_expr",
  splitBySign = FALSE,
  sampleAnnot = NULL,
  splitBySampleAnnot = FALSE,
  ...
)

Arguments

data

an object of type SummarizedExperiment. Output of the signatures functions.
nametype

character string saying the type of gene name ID (row names in data). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichSign

character vector saying the signatures to plot. These must be signatures computed with signifinder.
logCount

logical. If TRUE it shows logarithms of expression values.
whichAssay

integer scalar or string indicating which assay of data to use.
splitBySign

logical. If TRUE it splits rows by signatures.
sampleAnnot

vector containing samples' annotations.
splitBySampleAnnot

logical. If TRUE it splits columns by samples' annotations.
...

other parameters specific of the function Heatmap.

Value

A Heatmap-class object.

Examples

data(ovse)
geneHeatmapSignPlot(data = ovse, whichSign = "Ferroptosis_Ye")

Get Signature Gene List

Description

This function returns the list of genes of a signature.

Usage

getSignGenes(whichSign)

Arguments

whichSign

name of the signature. The names are those in column 'signature' from the table which is obtained by availableSignatures.

Value

A dataframe object with "SYMBOL" in the first column. Some signatures have also additional colums: "coeff" for coefficients that weigh the gene contributions; "class" for a classification that divides the signature in two or more groups. Few signatures have other specific columns.

Examples

getSignGenes("EMT_Miow")

Glioblastoma Cellular States Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

glioCellStateSign(
  dataset,
  nametype = "SYMBOL",
  whichAssay = "norm_expr",
  isMalignant = NULL,
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
isMalignant

logical vector of the same length of ncol(dataset), where TRUE states malignant cells and FALSE states non-malignant cells.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)

Glycolysis Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

glycolysisSign(
  dataset,
  nametype = "SYMBOL",
  author = "Zhang",
  whichAssay = "norm_expr"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
glycolysisSign(dataset = ovse)

Global Heatmap of Signatures' scores.

Description

Given one or multiple signatures, the function returns a heatmap of scores. Since each signature has its own method to compute the score then to plot several signatures together the scores are transformed into z-score, individually for each signature.

Usage

heatmapSignPlot(
  data,
  whichSign = NULL,
  clusterBySign = NULL,
  sampleAnnot = NULL,
  signAnnot = NULL,
  splitBySampleAnnot = FALSE,
  ...
)

Arguments

data

an object of type SummarizedExperiment. Output of the signatures functions.
whichSign

character vector saying the signatures to plot. If not specified, all the signatures inside data will be plotted. Other signatures not computed with signifinder can be added in the vector if they are also included in che colData section of data.
clusterBySign

character vector saying one or more signatures to use to cluster columns.
sampleAnnot

vector containing samples' annotations.
signAnnot

character vector of signature's annotations. One or more between: "signature", "topic", "tumor", "tissue".
splitBySampleAnnot

logical. If TRUE it splits columns by samples' annotations.
...

other parameters specific of the function Heatmap.

Value

A Heatmap-class object.

Examples

data(ovse)
heatmapSignPlot(data = ovse)

Homologous Recombination Deficiency Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

HRDSSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
HRDSSign(dataset = ovse)

Hypoxia Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

hypoxiaSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  whichAssay = "norm_expr"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
hypoxiaSign(dataset = ovse, inputType = "rnaseq")

ICB Response Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

ICBResponseSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
ICBResponseSign(dataset = ovse)

IFN-gamma Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

IFNSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
IFNSign(dataset = ovse)

Immune Cytolytic Activity Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

immuneCytSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  author = "Rooney",
  whichAssay = "norm_expr",
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
immuneCytSign(dataset = ovse, inputType = "rnaseq")

Immunogenic Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

immunoScoreSign(
  dataset,
  nametype = "SYMBOL",
  author = "Hao",
  inputType = "rnaseq",
  whichAssay = "norm_expr",
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
immunoScoreSign(dataset = ovse)

IPRES Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

IPRESSign(
  dataset,
  nametype = "SYMBOL",
  whichAssay = "norm_expr",
  hgReference = "hg38",
  ...
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".
...

other arguments passed on to the ssgseaParam function.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
IPRESSign(dataset = ovse)

IPSOV Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

IPSOVSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  whichAssay = "norm_expr",
  ...
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.
...

other arguments passed on to the ssgseaParam function.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
IPSOVSign(dataset = ovse)

ImmunoPhenoScore Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

IPSSign(
  dataset,
  nametype = "SYMBOL",
  whichAssay = "norm_expr",
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
IPSSign(dataset = ovse)

Immune-Related Genes Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

IRGSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
IRGSign(dataset = ovse)

Adult Intestinal Stem Cell Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

ISCSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "microarray",
  whichAssay = "norm_expr"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
ISCSign(dataset = ovse, inputType = "rnaseq")

Lipid Metabolism Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

lipidMetabolismSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
lipidMetabolismSign(dataset = ovse)

LRRC15 CAF Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

LRRC15CAFSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
LRRC15CAFSign(dataset = ovse)

Core Matrisome Gene signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

matrisomeSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
matrisomeSign(dataset = ovse)

Metastatic Melanoma Cellular States Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

melStateSign(
  dataset,
  nametype = "SYMBOL",
  whichAssay = "norm_expr",
  isMalignant = NULL,
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
isMalignant

logical vector of the same length of ncol(dataset), where TRUE states malignant cells and FALSE states non-malignant cells.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)

MITFlow/PTENneg Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

MITFlowPTENnegSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
MITFlowPTENnegSign(dataset = ovse)

Mitotic Index

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

mitoticIndexSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
mitoticIndexSign(dataset = ovse)

Melanocytic Plasticity Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

MPSSign(
  dataset,
  nametype = "SYMBOL",
  whichAssay = "norm_expr",
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
MPSSign(dataset = ovse)

Multiple Signatures Computation

Description

This function computes all the signatures for a specific 'inputType'. Further, it is possible to select specific signatures setting the 'tumor', the 'tissue' and/or the 'topic'.

Usage

multipleSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "rnaseq",
  whichAssay = "norm_expr",
  whichSign = NULL,
  tumor = NULL,
  tissue = NULL,
  topic = NULL,
  ...
)

Arguments

dataset

Expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character vector saying the type of data you are using. When working with bulk data this should be either one of "microarray" or "rnaseq". When working with single-cell data and spatial transcriptomics data this could be "sc" to compute only signatures developed by single-cell data or c("rnaseq", "sc") to compute all the signatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.
whichSign

character vector saying the signatures to compute.
tumor

character vector saying the tumor types. Signatures from that tumors will be computed (this can also be "pan-cancer").
tissue

character vector saying the tumor tissues. Signatures from that tissues will be computed (this can also be "pan-tissue").
topic

character vector saying signatures topics. Signatures having that topics will be computed.
...

other arguments passed on to the signature functions.

Value

A SummarizedExperiment object in which the signatures' scores are added in the colData section.

Examples

data(ovse)
multipleSign(dataset = ovse)
multipleSign(dataset = ovse, tissue = "ovary")

Scatterplot for a single signature

Description

Given signatures' scores, it returns a scatterplot of samples' scores and a barplot of the density distribution of samples' scores.

Usage

oneSignPlot(data, whichSign, statistics = NULL)

Arguments

data

an object of type SummarizedExperiment. Output of the signatures functions.
whichSign

character string saying the signature to plot. This must be a signature computed with signifinder.
statistics

character string saying the statistics to be plotted in the graph. Either one of "mean", "median" or "quantiles".

Value

A ggplot object.

Examples

data(ovse)
oneSignPlot(data = ovse, whichSign = "Ferroptosis_Ye")

Example expression data.

Description

This is an example dataset containing gene expression values (in normalized counts, TPM, CPM, and FPKM) of 40 ovarian cancer (OVC) patients extracted from the Cancer Genome Atlas (TCGA) database. This dataset should be used only with example purpose. RNA sequencing OVC data were retrieved using curatedTCGAData package. Data were then normalized with the betweenLaneNormalization function. To lighten the dataset, the consensusOVSign function was computed, which return 4 different scores, one for each OVC subtype (Chen et al, 2018, Clinical Cancer Research) and the 10 samples with the highest scores were selected for each subgroup. Further, only the genes used for the signatures computation were kept. Finally, all the signatures available in signifinder for OVC plus all the pan-cancer signatures were computed. Further details in signifinder/inst/scripts/howToGenerateOvse.Rmd.

Usage

data(ovse)

Format

An object of class SummarizedExperiment with 3180 rows and 40 columns.

passON Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

PassONSign(
  dataset,
  nametype = "SYMBOL",
  whichAssay = "norm_expr",
  hgReference = "hg38",
  ...
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".
...

other arguments passed on to the ssgseaParam function.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
PassONSign(dataset = ovse)

Pyroptosis Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

pyroptosisSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "rnaseq",
  author = "Ye",
  whichAssay = "norm_expr",
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
pyroptosisSign(dataset = ovse)

Ridgeline Plot

Description

Given multiple signatures, the function plots scores density distribution.

Usage

ridgelineSignPlot(
  data,
  whichSign = NULL,
  groupByAnnot = NULL,
  selectByAnnot = NULL,
  ...
)

Arguments

data

an object of type SummarizedExperiment. Output of the signatures functions.
whichSign

character vector saying the signatures to plot. If not specified, all the signatures inside data will be plotted. Other signatures not computed with signifinder can be added in the vector if they are also included in che colData section of data.
groupByAnnot

character vector containing samples' annotations.
selectByAnnot

character string saying the subgroup from 'groupByAnnot' used to compute the ridgeline plot.
...

other parameters specific of the functions geom_density_ridges and geom_density_ridges_gradient.

Value

A ggplot object.

Examples

data(ovse)
ridgelineSignPlot(data = ovse)

CD49fHi Basal Stem Cell Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

stemCellCD49fSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
stemCellCD49fSign(dataset = ovse)

Survival Plot

Description

Given a signature and samples' survival data, the function plots survival curves for that signature. This is a wrapper around survfit, that creates survival curves from a model formula. Here, the response variable in the formula is a survival object created by Surv. Survival curves are then passed to the ggsurvplot function. For details about the statistics see survfit and Surv.

Usage

survivalSignPlot(
  data,
  survData,
  whichSign,
  cutpoint = "mean",
  sampleAnnot = NULL,
  selectByAnnot = NULL
)

Arguments

data

an object of type SummarizedExperiment. Output of the signatures functions.
survData

a dataframe with samples on rows and two columns. The first column holds survival data of time, indicating the follow up times; the second holds data of the survival status, normally 0=alive and 1=dead. For further details check Surv function.
whichSign

character string saying the signature to plot. This must be a signature computed with signifinder.
cutpoint

a character string (one of: "median", "mean" and "optimal") or a numeric value, which divide samples between high scores and low scores. The function computes the threshold with the method indicated or employs the values directly supplied by the user. Based on that number, it divides samples. In case of "optimal" the maxstat.test function will be used to estimate the cutpoint which separates samples best.
sampleAnnot

a categorical vector containing samples' annotations named with samples names equal to the row names used in 'survData'.
selectByAnnot

character string saying the subgroup from 'sampleAnnot' used to compute the survival analysis.

Value

A ggplot object.

Examples

data(ovse)
mysurvData <- cbind(ovse$os, ovse$status)
rownames(mysurvData) <- rownames(SummarizedExperiment::colData(ovse))
survivalSignPlot(
    data = ovse,
    survData = mysurvData,
    whichSign = "Ferroptosis_Ye"
)

Pan-Fibroblast TGFB Response Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

TGFBSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
TGFBSign(dataset = ovse)

TinflamSign Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

TinflamSign(
  dataset,
  nametype = "SYMBOL",
  author = "Ayers",
  whichAssay = "norm_expr",
  hgReference = "hg38"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
author

character string saying the first author of the signature publication. Check it in availableSignatures.
whichAssay

integer scalar or string indicating which assay of dataset to use.
hgReference

character string saying the human reference genome. Either one of "hg19" or "hg38".

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
TinflamSign(dataset = ovse)

Tertiary Lymphoid Structures (TLS) Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

TLSSign(
  dataset,
  nametype = "SYMBOL",
  inputType = "rnaseq",
  whichAssay = "norm_expr"
)

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
inputType

character string saying the type of data you are using. Either one of "microarray" or "rnaseq".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
TLSSign(dataset = ovse)

VEGF Signature

Description

This signature is computed accordingly to the reference paper, to have more details explore the function availableSignatures.

Usage

VEGFSign(dataset, nametype = "SYMBOL", whichAssay = "norm_expr")

Arguments

dataset

Normalized expression values. A data frame or a matrix where rows correspond to genes and columns correspond to samples. Alternatively, an object of type SummarizedExperiment, SingleCellExperiment or SpatialExperiment where the normalized expression values should be in an assay called 'norm_expr'.
nametype

character string saying the type of gene name ID (row names in dataset). Either one of "SYMBOL", "ENTREZID" or "ENSEMBL".
whichAssay

integer scalar or string indicating which assay of dataset to use.

Value

If dataset is a SummarizedExperiment object, then scores are added in the colData section. If dataset is a data frame or a matrix, then a SummarizedExperiment object is created in which scores are added in the colData section.

Examples

data(ovse)
VEGFSign(dataset = ovse)