Package 'CTexploreR'

Title: Explores Cancer Testis Genes
Description: The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes' main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.
Authors: Axelle Loriot [aut, cre] , Julie Devis [aut] , Anna Diacofotaki [ctb], Charles De Smet [ths], Laurent Gatto [aut, ths]
Maintainer: Axelle Loriot <[email protected]>
License: Artistic-2.0
Version: 1.3.0
Built: 2024-11-19 03:34:02 UTC
Source: https://github.com/bioc/CTexploreR

Help Index

All genes description table

Description

All genes description, imported from CTdata

Usage

all_genes

Format

A tibble object with 24488 rows and 47 columns.

  • Rows correspond to CT genes

  • Columns give CT genes characteristics

Details

See CTdata::all_genes documentation for details

Value

A tibble of all 24 488 genes with their characteristics

Source

See scripts/make_all_genes.R in CTdata for details on how this list was created.

Examples

all_genes

Gene expression in CCLE Tumors

Description

Plots an expression heatmap of genes in CCLE tumor cell lines.

Usage

CCLE_expression(
  genes = NULL,
  type = NULL,
  units = c("TPM", "log_TPM"),
  include_CTP = FALSE,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
type

character() describing the tumor cell line(s) type to be plotted. Allowed cell lines are "Ovarian", "Leukemia", "Colorectal", "Skin", "Lung", "Bladder", "Kidney", "Breast", "Pancreatic", "Myeloma", "Brain", "Sarcoma", "Lymphoma", "Bone", "Neuroblastoma", "Gastric", "Uterine", "Head_and_Neck", "Bile_Duct" and "Esophageal".
units

character(1) with expression values unit. Can be "TPM" (default) or "log_TPM" (log(TPM + 1))
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
values_only

logical(1). If TRUE, values are returned instead of the heatmap (FALSE by default).

Value

A heatmap of selected genes in CCLE cell lines from specified type. If values_only is TRUE, expression values are returned instead.

Examples

## Not run: 
CCLE_expression(
    genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "MAGEA10"),
    type = c("Skin", "Lung"), units = "log_TPM")

## End(Not run)

Check spelling of entered variables

Description

Checks the spelling of a vector of entered variable(s) comparing it to a vector of valid names, and removes the ones that are absent from the vector of valid names.

Usage

check_names(variable, valid_vector)

Arguments

variable

character() containing the names of variables to check.
valid_vector

character() with valid variable names.

Value

A character with valid variables.

Examples

CTexploreR:::check_names(
    variable = c("Ovarian", "leukemia", "wrong_name"),
    valid_vector = c("ovarian", "leukemia")
)

Gene correlations in CCLE cancer cell lines

Description

A function that uses expression data from CCLE cell lines and highlights genes correlated (or anti-correlated) with specified CT gene. Genes with a correlation coefficient above threshold are colored in red if they are CT genes or in blue, if not.

Usage

CT_correlated_genes(gene, corr_thr = 0.5, values_only = FALSE)

Arguments

gene

CT gene selected
corr_thr

numeric(1) with default 0.5. Genes with an absolute correlation coefficient (Pearson) higher than this threshold will be highlighted.
values_only

logical(1), FALSE by default. If TRUE, the function will return the correlation coefficients with all genes instead of the plot.

Value

A plot where each dots represent the correlation coefficients (Pearson) between genes and the specified CT gene (entered as input). Genes with a correlation coefficient above threshold are colored in red if they are CT genes or in blue, if not. If values_only = TRUE, all correlations coefficients are returned instead.

Examples

## Not run: 
CT_correlated_genes(gene = "MAGEA3")

## End(Not run)

CT genes description table

Description

Cancer-Testis (CT) genes description, imported from CTdata

Usage

CT_genes

Format

A tibble object with 280 rows and 47 columns.

  • Rows correspond to CT genes

  • Columns give CT genes characteristics

Details

See CTdata::CT_genes documentation for details

Value

A tibble of all 280 CT and CTP genes with their characteristics

Source

See scripts/make_CT_genes.R in CTdata for details on how this list of curated CT genes was created.

Examples

CT_genes

Gene expression in cells treated or not by a demethylating agent

Description

Plots a heatmap of normalised gene counts (log-transformed) in a selection of cells treated or not by 5-Aza-2'-Deoxycytidine (DAC), a demethylating agent.

Usage

DAC_induction(
  genes = NULL,
  multimapping = TRUE,
  include_CTP = FALSE,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT specific genes.
multimapping

logical(1) defining whether to use multi-mapped gene expression dataset CTdata::DAC_treated_cells_multimapping or DAC_treated_cells. Default is TRUE.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
values_only

logical(1). If TRUE, the function will return the gene normalised logcounts in all samples instead of the heatmap. Default is FALSE.

Details

RNAseq data from cells treated or not with 5-aza downloaded from SRA. (SRA references and information about cell lines and DAC treatment are stored the colData of DAC_treated_cells). Data was processed using a standard RNAseq pipeline. hisat2 was used to align reads to grch38 genome. featurecounts was used to assign reads to genes. Note that -M parameter was used or not to allow or not counting multi-mapping reads.

Value

A heatmap of selected genes in cells treated or not by a demethylating agent. If values_only is TRUE, gene normalised logcounts are returned instead.

Examples

DAC_induction(genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "CTAG1A"))
DAC_induction(genes = c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEA6", "CTAG1A",
    multimapping = FALSE))

Gene expression in human embryos

Description

Plots a heatmap of genes expression in human early embryos, from "Petropoulos" scRNAseq dataset ("Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos". Petropoulos et al., Cell 2016) or from "Zhu" scRNAseq dataset ("Single-cell DNA methylome sequencing of human preimplantation embryos". Zhu et al. Nat genetics 2018)

Usage

embryo_expression(
  dataset = c("Petropoulos", "Zhu"),
  genes = NULL,
  include_CTP = FALSE,
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

dataset

character. Indicates which scRNAseq dataset to use. Either Petropoulos or Zhu, no default.
genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
scale_lims

⁠vector of length 2⁠ setting the lower and upper limits of the heatmap colorbar. By default, the lower limit is 0, and the upper limit corresponds to the third quartile of the logcounts values.
values_only

logical(1). If TRUE, the function will return the SingleCellExperiment instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in single cells from embryos. If values_only = TRUE, a SingleCellExperiment is returned instead.

Examples

## Not run: 
embryo_expression(dataset = "Petropoulos", include_CTP = FALSE)
embryo_expression(dataset = "Zhu", include_CTP = FALSE)

## End(Not run)

Promoter methylation of any gene in early embryos

Description

Plots a heatmap of mean promoter methylation levels of any genes in early embryos, using WGSB data from ("Single-cell DNA methylome sequencing of human preimplantation embryos". Zhu et al. Nat genetics 2018). Methylation levels in tissues correspond to the mean methylation of CpGs located in range of 1000 pb upstream and 500 pb downstream from gene TSS.

Usage

embryos_mean_methylation(
  genes = NULL,
  stage = c("GV Oocyte", "MII Oocyte", "Sperm", "Zygote", "2-cell", "4-cell", "8-cell",
    "Morula", "Blastocyst", "Post-implantation"),
  include_CTP = FALSE,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
stage

character defining the cell types to be plotted. Can be "GV Oocyte", "MII Oocyte", "Sperm", "Zygote", "2-cell", "4-cell", "8-cell", "Morula", "Blastocyst", "Post-implantation".
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
values_only

logical(1), FALSE by default. If TRUE, the function will return the methylation values in all samples instead of the heatmap.

Value

Heatmap of mean promoter methylation of any gene in embryos. If values_only = TRUE, a RangedSummarizedExperiment with methylation values is returned instead.

Examples

embryos_mean_methylation()
embryos_mean_methylation(c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEC2", "MAGEB16"),
stage = c( "MII Oocyte", "Sperm", "Zygote", "2-cell", "4-cell", "8-cell", 
"Morula"))

Gene expression in fetal germ cells

Description

Plots a heatmap of genes expression in fetal germ cells, using scRNAseq data from "Single-cell roadmap of human gonadal development" (Garcia-Alonso, Nature 2022)

Usage

fetal_germcells_expression(
  genes = NULL,
  include_CTP = FALSE,
  ncells_max = 200,
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
ncells_max

integer(1) Sets the number of each cell type to represent on the heatmap (these cells will be randomly selected among each cell type) (set to 200 by default). If NULL, all cells are displayed.
scale_lims

⁠vector of length 2⁠ setting the lower and upper limits of the heatmap colorbar. By default, the lower limit is 0, and the upper limit corresponds to the third quartile of the logcounts values.
values_only

logical(1). If TRUE, the function will return the SingleCellExperiment instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in single cells from fetal germ cells. If values_only = TRUE, a SingleCellExperiment is returned instead.

Examples

## Not run: 
fetal_germcells_expression(include_CTP = FALSE, ncells_max = 100)

## End(Not run)

Promoter methylation of any gene in fetal germ cells

Description

Plots a heatmap of mean promoter methylation levels of any genes in fetal germ cells, using WGSB data from "Dissecting the epigenomic dynamics of human fetal germ cell development at single-cell resolution" (Li et al. 2021). Methylation levels in tissues correspond to the mean methylation of CpGs located in range of 1000 pb upstream and 500 pb downstream from gene TSS.

Usage

fetal_germcells_mean_methylation(
  genes = NULL,
  include_CTP = FALSE,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
values_only

logical(1), FALSE by default. If TRUE, the function will return the methylation values in all samples instead of the heatmap.

Value

Heatmap of mean promoter methylation of any gene in normal tissues. If values_only = TRUE, a SummarizeExperiment with methylation values is returned instead.

Examples

fetal_germcells_mean_methylation()
fetal_germcells_mean_methylation(c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEC2"))

Gene expression in normal tissues (GTEx)

Description

Plots an expression heatmap of genes in normal tissues (GTEx database).

Usage

GTEX_expression(
  genes = NULL,
  units = c("TPM", "log_TPM"),
  include_CTP = FALSE,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
units

character(1) with expression values unit. Can be "TPM" (default) or "log_TPM" (log(TPM + 1)).
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
values_only

logical(1). If TRUE, the function will return the expression values in all samples instead of the heatmap. Default is FALSE.

Value

A heatmap of selected genes expression in normal tissues. If values_only = TRUE, expression values are returned instead.

Examples

GTEX_expression(units = "log_TPM")
GTEX_expression(genes = c("MAGEA1", "MAGEA3"), units = "log_TPM")

Gene expression in human embryonic stem cells

Description

Plots a heatmap of genes expression in human embryonic stem cells, using RNAseq data downloaded from Encode database.

Usage

hESC_expression(
  genes = NULL,
  include_CTP = FALSE,
  units = c("TPM"),
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
units

character(1) with expression values unit. Can be "TPM" (default) or "log_TPM" (log(TPM + 1)).
scale_lims

⁠vector of length 2⁠ setting the lower and upper limits of the heatmap colorbar. By default, the lower limit is 0, and the upper limit corresponds to the third quartile of the logcounts values.
values_only

logical(1). If TRUE, the function will return the SingleCellExperiment instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in single cells from human embryonic stem cells. If values_only = TRUE, a SummarizedExperiment is returned instead.

Examples

## Not run: 
hESC_expression(include_CTP = FALSE, units = "log_TPM",
                  values_only = FALSE)

## End(Not run)

Promoter methylation of any gene in hESC

Description

Plots a heatmap of mean promoter methylation levels of any genes in human embryonic cell lines. WGBS methylation data was downloaded from Encode. Methylation levels in tissues correspond to the mean methylation of CpGs located in range of 1000 pb upstream and 200 pb downstream from gene TSS.

Usage

hESC_mean_methylation(
  genes = NULL,
  include_CTP = FALSE,
  values_only = FALSE,
  na.omit = TRUE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
values_only

logical(1), FALSE by default. If TRUE, the function will return the methylation values in all samples instead of the heatmap.
na.omit

logical(1) specifying if genes with missing methylation values in some tissues should be removed (TRUE by default). Note that no gene clustering will be done when methylation values are missing.

Value

Heatmap of mean promoter methylation of any gene in hESC. If values_only = TRUE, a SummarizedExperiment cobtaining methylation values is returned instead.

Examples

## Not run: 
hESC_mean_methylation()

## End(Not run)

Gene expression in different human cell types

Description

Plots a heatmap of genes expression in the different human cell types based on scRNAseq data obtained from the Human Protein Atlas (https://www.proteinatlas.org)

Usage

HPA_cell_type_expression(
  genes = NULL,
  units = c("scaled", "TPM", "log_TPM"),
  include_CTP = FALSE,
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
units

character(1) with expression values unit. Can be "TPM", "log_TPM" (log(TPM + 1)) or "scaled" (scaled TPM values). Default is "scaled".
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
scale_lims

⁠vector of length 2⁠ setting the lower and upper limits of the heatmap colorbar.
values_only

logical(1). If TRUE, the function will return the SummarizedExperiment instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in different human cell types. If values_only = TRUE, a SummarizedExperiment instead of the heatmap is returned instead.

Examples

HPA_cell_type_expression(
    genes = NULL, units = "scaled", scale_lims = NULL,
    values_only = FALSE)
HPA_cell_type_expression(
    genes = c("MAGEA1", "MAGEA3", "MAGEA4"),
    units = "TPM", scale_lims = c(0, 50),
    values_only = FALSE)

Expression values (TPM) of genes in normal tissues with or without multimapping

Description

Plots a heatmap of gene expression values in a set of normal tissues. Expression values (in TPM) have been evaluated by either counting or discarding multi-mapped reads. Indeed, many CT genes belong to gene families from which members have identical or nearly identical sequences. Some CT can only be detected in RNAseq data in which multimapping reads are not discarded.

Usage

normal_tissue_expression_multimapping(
  genes = NULL,
  include_CTP = FALSE,
  multimapping = TRUE,
  units = c("TPM", "log_TPM"),
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
multimapping

logical(1) that specifies if returned expression values must take into account or not multi-mapped reads. TRUE by default.
units

character(1) with expression values unit. Can be "TPM" (default) or "log_TPM" (log(TPM + 1)).
values_only

logical(1). If TRUE, the function will return the expression values in all samples instead of the heatmap. Default is FALSE.

Details

RNAseq data from a set of normal tissues were downloaded from Encode. (see inst/scripts/make_CT_normal_tissues_multimapping.R for fastq references) Fastq files were processed using a standard RNAseq pipeline including FastQC for the quality control of the raw data, and trimmomatic to remove low quality reads and trim the adapter from the sequences. hisat2 was used to align reads to grch38 genome. featurecounts was used to assign reads to genes using Homo_sapiens.GRCh38.105.gtf.

Two different pipelines were run in order to remove or not multi-mapping reads. When multimapping was allowed, hisat2 was run with -k 20 parameter (reports up to 20 alignments per read), and featurecounts was run with -M parameter (multi-mapping reads are counted).

Value

A heatmap of selected gene expression values in a set of normal tissues calculated by counting or discarding multi-mapped reads. If values_only = TRUE, gene expression values are returned instead.

Examples

normal_tissue_expression_multimapping(
    genes = c("GAGE13", "CT45A6", "NXF2", "SSX2", "CTAG1A",
    "MAGEA3", "MAGEA6"), multimapping = FALSE)
normal_tissue_expression_multimapping(
    genes = c("GAGE13", "CT45A6", "NXF2", "SSX2", "CTAG1A",
    "MAGEA3", "MAGEA6"), multimapping = TRUE)

Promoter methylation of any gene in normal tissues

Description

Plots a heatmap of mean promoter methylation levels of any genes in normal tissues. Methylation levels in tissues correspond to the mean methylation of CpGs located in range of 1000 pb upstream and 200 pb downstream from gene TSS.

Usage

normal_tissues_mean_methylation(
  genes = NULL,
  include_CTP = FALSE,
  values_only = FALSE,
  na.omit = TRUE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
values_only

logical(1), FALSE by default. If TRUE, the function will return the methylation values in all samples instead of the heatmap.
na.omit

logical(1) specifying if genes with missing methylation values in some tissues should be removed (TRUE by default). Note that no gene clustering will be done when methylation values are missing.

Value

Heatmap of mean promoter methylation of any gene in normal tissues. If values_only = TRUE, methylation values are returned instead.

Examples

normal_tissues_mean_methylation()
normal_tissues_mean_methylation(c("MAGEA1", "MAGEA2", "MAGEA3", "MAGEA4"))
normal_tissues_mean_methylation(c("MAGEA1", "MAGEA2", "MAGEA3", "MAGEA4"),
    na.omit = FALSE)

Methylation of CpGs located in promoters in normal tissues

Description

Plots a heatmap of the methylation of CpGs located in a promoter, in normal tissues. X-axis corresponds to the CpGs position (related to TSS).

Usage

normal_tissues_methylation(
  gene,
  nt_up = 1000,
  nt_down = 200,
  values_only = FALSE
)

Arguments

gene

Name of selected gene
nt_up

Number of nucleotides upstream the TSS to analyse (by default 1000, maximum value 5000)
nt_down

Number of nucleotides downstream the TSS to analyse (by default 200, maximum value 5000)
values_only

Boolean (FALSE by default). If set to TRUE, the function will return the methylation values of all cytosines in the promoter instead of the heatmap.

Value

Heatmap of the methylation of CpGs located in a promoter, in normal tissues. If values_only = TRUE, methylation values are returned instead.

Examples

normal_tissues_methylation(gene = "TDRD1", 1000, 0)

Gene expression in oocytes

Description

Plots a heatmap of genes expression in oocytes, using scRNAseq data from "Decoding dynamic epigenetic landscapes in human oocytes using single-cell multi-omics sequencing" (Yan et al. Cell Stem Cell 2021)

Usage

oocytes_expression(
  genes = NULL,
  include_CTP = FALSE,
  ncells_max = 200,
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
ncells_max

integer(1) Sets the number of each cell type to represent on the heatmap (these cells will be randomly selected among each cell type) (set to 200 by default). If NULL, all cells are displayed.
scale_lims

⁠vector of length 2⁠ setting the lower and upper limits of the heatmap colorbar. By default, the lower limit is 0, and the upper limit corresponds to the third quartile of the logcounts values.
values_only

logical(1). If TRUE, the function will return the SingleCellExperiment instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in single cells from human oocytes. If values_only = TRUE, a SingleCellExperiment is returned instead.

Examples

## Not run: 
oocytes_expression(include_CTP = FALSE, ncells_max = 100,
                  values_only = FALSE)

## End(Not run)

Prepare methylation and expression data of a gene in TCGA tumors

Description

Creates a Dataframe giving for each TCGA sample, the methylation level of a gene (mean methylation of probes located in its promoter) and the expression level of the gene (TPM value).

Usage

prepare_TCGA_methylation_expression(
  tumor = "all",
  gene = NULL,
  nt_up = NULL,
  nt_down = NULL,
  include_normal_tissues = FALSE
)

Arguments

tumor

character defining the TCGA tumor type. Can be one of "SKCM", "LUAD", "LUSC", "COAD", "ESCA", "BRCA", "HNSC", or "all" (default).
gene

character selected CT gene.
nt_up

numeric(1) indicating the number of nucleotides upstream the TSS to define the promoter region (1000 by default)
nt_down

numeric(1) indicating the number of nucleotides downstream the TSS to define the promoter region (200 by default)
include_normal_tissues

logical(1). If TRUE, the function will include normal peritumoral tissues in addition to tumoral samples. Default is FALSE.

Value

a Dataframe giving for each TCGA sample, the methylation level of a gene (mean methylation of probes located in its promoter) and the expression level of the gene (TPM value). The number of probes used to estimate the methylation level is also reported.

Examples

## Not run: 
  CTexploreR:::prepare_TCGA_methylation_expression("LUAD", gene = "TDRD1")

## End(Not run)

Determine font size

Description

Gives the fontsize to use for the heatmap based on the matrix's dimension.

Usage

set_fontsize(matrix)

Arguments

matrix

matrix containing the data to visualise

Value

A logical number that is the fontsize to use

Examples

CTexploreR:::set_fontsize(matrix(1:3, 9,8))

Subset databases

Description

Check the presence of the genes in the database then subsets the database to only keep these genes' data.

Usage

subset_database(variable = NULL, data, include_CTP = FALSE)

Arguments

variable

character() containing the names genes to keep in the data. The default value, NULL, takes CT (specific) genes
data

⁠Summarized Experiment⁠ or SingleCellExperiment object with valid variable names.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).

Value

A ⁠Summarized Experiment⁠ or SingleCellExperiment object with only the variables data

Examples

CTexploreR:::subset_database(variable = "MAGEA1", data = CTdata::GTEX_data())

Gene expression in TCGA tumors

Description

Plots a heatmap of genes expression in TCGA samples (peritumoral and tumor samples when a specific tumor type is specified, or tumor samples only when tumor option is set to "all")

Usage

TCGA_expression(
  tumor = "all",
  genes = NULL,
  include_CTP = FALSE,
  units = c("TPM", "log_TPM"),
  values_only = FALSE
)

Arguments

tumor

character defining the TCGA tumor type. Can be one of "SKCM", "LUAD", "LUSC", "COAD", "ESCA", "BRCA", "HNSC", or "all" (default).
genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
units

character(1) with expression values unit. Can be "TPM" (default) or "log_TPM" (log(TPM + 1)).
values_only

logical(1). If TRUE, the function will return the expression values in all samples instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in TCGA samples. If values_only = TRUE, TPM expression data is returned instead.

Examples

## Not run: 
TCGA_expression(
    tumor = "LUAD", genes = c("MAGEA1", "MAGEA3"),
    units = "log_TPM")

## End(Not run)

Methylation-Expression correlation of any genes in TCGA samples

Description

Plots the correlation between methylation and expression values of a gene in TCGA samples.

Usage

TCGA_methylation_expression_correlation(
  tumor = "all",
  gene = NULL,
  nt_up = 1000,
  nt_down = 200,
  min_probe_number = 3,
  include_normal_tissues = FALSE,
  values_only = FALSE
)

Arguments

tumor

character defining the TCGA tumor type. Can be one of "SKCM", "LUAD", "LUSC", "COAD", "ESCA", "BRCA", "HNSC", or "all" (default).
gene

character selected gene.
nt_up

numeric(1) indicating the number of nucleotides upstream the TSS to define the promoter region (1000 by default)
nt_down

numeric(1) indicating the number of nucleotides downstream the TSS to define the promoter region (200 by default)
min_probe_number

numeric(1) indicating the minimum number of probes (with methylation values) within the selected region to calculate its mean methylation level. Default is 3.
include_normal_tissues

logical(1). If TRUE, the function will include normal peritumoral tissues in addition to tumoral samples. Default is FALSE.
values_only

logical(1). If TRUE, the function will return the methylation and expression values in TCGA samples instead of the heatmap. Default is FALSE.

Details

The coefficient of correlation is set to NA if no probes are found in promoter regions or if less than 1% of tumors are positive (TPM >= 1) for the gene.

Value

A scatter plot representing for each TCGA sample, gene expression and mean methylation values of probe(s) located in its promoter region (defined as 1000 nucleotides upstream TSS and 200 nucleotides downstream TSS by default). If values_only = TRUE, methylation and expression values are returned in a tibble instead.

Examples

## Not run: 
TCGA_methylation_expression_correlation("LUAD", gene = "TDRD1")

## End(Not run)

Gene expression in testis cells

Description

Plots a heatmap of genes expression in the different types of testis cells, using scRNAseq data from "The adult human testis transcriptional cell atlas" (Guo et al. 2018)

Usage

testis_expression(
  cells = c("all", "germ_cells", "somatic_cells", "SSC", "Spermatogonia",
    "Early_spermatocyte", "Late_spermatocyte", "Round_spermatid", "Elongated_spermatid",
    "Sperm1", "Sperm2", "Macrophage", "Endothelial", "Myoid", "Sertoli", "Leydig"),
  genes = NULL,
  include_CTP = FALSE,
  scale_lims = NULL,
  values_only = FALSE
)

Arguments

cells

character defining the testis cell types to be plotted. Can be "germ_cells", "somatic_cells", "all" (default), or any or a combination of "SSC", "Spermatogonia", "Early_spermatocyte", "Late_spermatocyte", "Round_spermatid", "Elongated_spermatid", "Sperm1", "Sperm2", "Macrophage", "Endothelial", "Myoid", "Sertoli", "Leydig".
genes

character naming the selected genes. The default value, NULL, takes all CT (specific) genes.
include_CTP

logical(1) If TRUE, CTP genes are included. (FALSE by default).
scale_lims

⁠vector of length 2⁠ setting the lower and upper limits of the heatmap colorbar. By default, the lower limit is 0, and the upper limit corresponds to the third quartile of the logcounts values.
values_only

logical(1). If TRUE, the function will return the SingleCellExperiment instead of the heatmap. Default is FALSE.

Value

A heatmap of selected CT genes expression in single cells from adult testis. If values_only = TRUE, a SingleCellExperiment is returned instead.

Examples

## Not run: 
testis_expression(cells = "germ_cells",
                  genes = c("MAGEA1", "MAGEA3", "MAGEA4"))

## End(Not run)