Package 'CoSIA'

Title: An Investigation Across Different Species and Tissues
Description: Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. CoSIA uses the Coefficient of Variation and Shannon Entropy and Specificity to calculate transcriptome diversity and variation. CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison.
Authors: Anisha Haldar [aut] , Vishal H. Oza [aut] , Amanda D. Clark [cre, aut] , Nathaniel S. DeVoss [aut] , Brittany N. Lasseigne [aut]
Maintainer: Amanda D. Clark <[email protected]>
License: MIT + file LICENSE
Version: 1.5.4
Built: 2024-10-26 03:27:26 UTC
Source: https://github.com/bioc/CoSIA

Help Index

CoSIAn Class S4 Object

Description

This Class is used to specify the information needed to conduct analysis using CoSIA's other methods. An object of this class will pass as an argument to other methods in CoSIA

Value

CoSIAn object

Slots

gene_set

character. A singular gene or a list of genes.

i_species

character. The species corresponding to gene_set.

input_id

character. The type of id corresponding to gene_set.

o_species

character. The singular or list of species that the gene set is being converted to.

output_ids

character. The singular or list of id types that the gene set is being converted to.

mapping_tool

character. The mapping tool, BiomaRt or annotationDBI, being used to map the conversion between IDs.

ortholog_database

character. The ortholog database, HomoloGene or NCBIOrtho, being used to map the conversion between species.

converted_id

data frame. Output of getConversion.

map_tissues

character. A list of tissues being investigated.

map_species

character. A list of species being investigated.

gex

data frame. Output of gene expression data.

metric_type

character. A list of possible metric the user wants to calculate.

metric

data frame. Output of coefficient of variation of gene expression data.

Constructor for the CoSIAn Object

Description

The CoSIAn constructor creates a CoSIAn object from character vector(s).

Usage

CoSIAn(
  gene_set,
  i_species,
  input_id,
  o_species,
  output_ids,
  mapping_tool = "annotationDBI",
  ortholog_database = "HomoloGene",
  map_tissues,
  map_species,
  metric_type
)

Arguments

gene_set

A singular gene or a list of genes.
i_species

The species corresponding to gene_set.
input_id

The type of id corresponding to gene_set.
o_species

The singular or list of species that the gene set is being converted to.
output_ids

The singular or list of id types that the gene set is being converted to.
mapping_tool

The mapping tool, BiomaRt or annotationDBI, being used to map the conversion between IDs.
ortholog_database

The ortholog database, HomoloGene or NCBIOrtho, being used to map the conversion between species.
map_tissues

A list of tissues being investigated
map_species

A list of species being investigated
metric_type

A list of possible metric the user wants to calculate.

Value

An S4 CoSIAn object with character vector(s) as slots.

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c(
        "ENSG00000008710", "ENSG00000118762",
        "ENSG00000152217"
    ), i_species = "h_sapiens", input_id = "Ensembl_id",
    o_species = c(
        "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio",
        "c_elegans", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("m_musculus"), 
    metric_type = "DS_Gene"
)

getConversion Generic

Description

getConversion Generic

Usage

getConversion(object)

Arguments

object

CoSIAn object with all user accessible slots filled

Value

initializes a generic function for getConversion as preparation for defining the getConversion Method

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id",
    o_species = c(
        "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio",
        "c_elegans", "r_norvegicus"
    ),
    output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI",
    ortholog_database = "HomoloGene", map_tissues = "heart",
    map_species = c("m_musculus"), metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)

getConversion Method

Description

getConversion Method

Usage

## S4 method for signature 'CoSIAn'
getConversion(object)

Arguments

object

CoSIAn object with all user accessible slots filled

Value

CoSIAn object with converted_id slot filled

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id",
    o_species = c(
        "d_melanogaster", "m_musculus", "h_sapiens", "d_rerio",
        "c_elegans", "r_norvegicus"
    ),
    output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI",
    ortholog_database = "HomoloGene", map_tissues = "heart",
    map_species = c("m_musculus"), metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)

getGEx Generic

Description

getGEx Generic

Usage

getGEx(object)

Arguments

object

CoSIAn object with all user accessible slots filled with converted_id slot filled

Value

initializes a generic function for getGEx as preparation for defining the getGEx Method

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id",
    o_species = c(
        "h_sapiens", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("r_norvegicus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_gex <- getGEx(Kidney_gene_conversion)

getGEx Method

Description

getGEx Method

Usage

## S4 method for signature 'CoSIAn'
getGEx(object)

Arguments

object

CoSIAn object with all user accessible slots filled with converted_id slot filled

Value

CoSIAn Object with gex slot filled

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id",
    o_species = c(
        "h_sapiens", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("r_norvegicus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_gex <- getGEx(Kidney_gene_conversion)

getGExMetrics Generic

Description

getGExMetrics Generic

Usage

getGExMetrics(object)

Arguments

object

CoSIAn object with all user accessible slots filled with converted_id slot filled

Value

initializes a generic function for getGExMetrics as preparation for defining the getGExMetrics Method

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "h_sapiens", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("r_norvegicus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)

getGExMetrics Method

Description

getGExMetrics Method

Usage

## S4 method for signature 'CoSIAn'
getGExMetrics(object)

Arguments

object

CoSIAn object with all user accessible slots filled with converted_id slot filled

Value

CoSIAn Object with metric slot filled

References

Kohl M (2022). MKdescr: Descriptive Statistics. R package version 0.8, https://github.com/stamats/MKdescr.

Zhang JD, Hatje K, Sturm G, Broger C, Ebeling M, Burtin M, Terzi F, Pomposiello SI, Badi L (2017). “Detect tissue heterogeneity in gene expression data with BioQC.” BMC Genomics, 18(1), 277. http://accio.github.io/BioQC/.

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "h_sapiens", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("r_norvegicus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)

getTissues

Description

getTissues

Usage

getTissues(species)

Arguments

species

name of a species or multiple species that you want to get available tissue list for

Value

list of tissues that are common/available among the species or multiple species inputted

Examples

tissue <- getTissues(c("m_musculus"))

plotCVGEx Generic

Description

plotCVGEx Generic

Usage

plotCVGEx(object)

Arguments

object

CoSIAn object with all user accessible slots filled in as well as the converted_id and metric slot filled

Value

initializes a generic function for plotCVGEx as preparation for defining the plotCVGEx Method

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "h_sapiens", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = c("adult mammalian kidney","heart"), 
    map_species = c("h_sapiens", "r_norvegicus"),
    metric_type = "CV_Tissue"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
plot <- plotCVGEx(Kidney_gene_metric)

plotCVGEx Method

Description

plotCVGEx Method

Usage

## S4 method for signature 'CoSIAn'
plotCVGEx(object)

Arguments

object

CoSIAn object with all user accessible slots filled in as well as the converted_id and metric slot filled

Value

plot object

References

Dot plot in R with the dotchart function [with examples]. R CODER. (2020, November 20). Retrieved from https://r-coder.com/dot-plot-r/

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "h_sapiens", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = c("adult mammalian kidney","heart"), 
    map_species = c("h_sapiens", "r_norvegicus"),
    metric_type = "CV_Tissue"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
plot <- plotCVGEx(Kidney_gene_metric)

plotDSGEx Generic

Description

plotDSGEx Generic

Usage

plotDSGEx(object)

Arguments

object

CoSIAn object with all user accessible slots filled in as well as the converted_id and metric slot filled

Value

initializes a generic function for plotDSGEx as preparation for defining the plotDSGEx Method

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "d_melanogaster", "m_musculus",
        "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("m_musculus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
plotDSGEx(Kidney_gene_metric)

plotDSGEx Method

Description

plotDSGEx Method

Usage

## S4 method for signature 'CoSIAn'
plotDSGEx(object)

Arguments

object

CoSIAn object with all user accessible slots filled in as well as the converted_id and metric slot filled

Value

plot object

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "d_melanogaster", "m_musculus",
        "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("m_musculus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_metric <- getGExMetrics(Kidney_gene_conversion)
plotDSGEx(Kidney_gene_metric)

plotSpeciesGEx Generic

Description

plotSpeciesGEx Generic

Usage

plotSpeciesGEx(object, single_tissue, single_gene)

Arguments

object

CoSIAn object with all user accessible slots filled in as well as the converted_id and gex slot filled
single_tissue

one tissue that the user wants to investigate across the mapped species
single_gene

one ensembl id that the user wants to investigate across the mapped species

Value

initializes a generic function for plotSpeciesGEx as preparation for defining the plotSpeciesGEx Method

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "d_melanogaster", "m_musculus",
        "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("m_musculus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_gex <- getGEx(Kidney_gene_conversion)
plotSpeciesGEx(Kidney_gene_gex, "liver", "ENSG00000008710")

plotSpeciesGEx Method

Description

plotSpeciesGEx Method

Usage

## S4 method for signature 'CoSIAn'
plotSpeciesGEx(object, single_tissue, single_gene)

Arguments

object

CoSIAn object with all user accessible slots filled in as well as the converted_id and gex slot filled
single_tissue

one tissue that the user wants to investigate across the mapped species
single_gene

one ensembl id that the user wants to investigate across the mapped species

Value

plot object

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "d_melanogaster", "m_musculus",
        "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("m_musculus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_gex <- getGEx(Kidney_gene_conversion)
plotSpeciesGEx(Kidney_gene_gex, "liver", "ENSG00000008710")

plotTissueGEx Generic

Description

plotTissueGEx Generic

Usage

plotTissueGEx(object, single_species, single_gene)

Arguments

object

CoSIAn object with all user accessible slots filled in as well as the converted_id and gex slot filled
single_species

one species that the user wants to investigate across the mapped tissues
single_gene

one ensembl id that the user wants to investigate across the mapped tissues

Value

initializes a generic function for plotTissueGEx as preparation for defining the plotTissueGEx Method

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "d_melanogaster", "m_musculus",
        "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart",
    map_species = c("m_musculus"), metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_gex <- getGEx(Kidney_gene_conversion)
plotTissueGEx(Kidney_gene_gex, "m_musculus", "ENSG00000008710")

plotTissueGEx Method

Description

plotTissueGEx Method

Usage

## S4 method for signature 'CoSIAn'
plotTissueGEx(object, single_species, single_gene)

Arguments

object

CoSIAn object with all user accessible slots filled in as well as the converted_id and gex slot filled
single_species

one species that the user wants to investigate across the mapped tissues
single_gene

one ensembl id that the user wants to investigate across the mapped tissues

Value

plot object

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000118762", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id", o_species = c(
        "d_melanogaster", "m_musculus",
        "h_sapiens", "d_rerio", "c_elegans", "r_norvegicus"
    ), output_ids = c("Ensembl_id", "Symbol"),
    mapping_tool = "annotationDBI", ortholog_database = "HomoloGene",
    map_tissues = "heart", map_species = c("m_musculus"),
    metric_type = "DS_Gene"
)
Kidney_gene_conversion <- CoSIA::getConversion(Kidney_Genes)
Kidney_gene_gex <- getGEx(Kidney_gene_conversion)
plotTissueGEx(Kidney_gene_gex, "m_musculus", "ENSG00000008710")

viewCoSIAn Generics

Description

viewCoSIAn Generics

Usage

viewCoSIAn(object, slot_name)

Arguments

object

CoSIAn object with all user accessible slots filled
slot_name

name of output slots

Value

initializes a generic function for viewCoSIAn as preparation for defining the viewCoSIAn Method

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id",
    o_species = c(
        "d_melanogaster"
    ),
    output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI",
    ortholog_database = "HomoloGene", map_tissues = "heart",
    map_species = c("d_melanogaster"), metric_type = "DS_Gene"
)
viewCoSIAn(Kidney_Genes, "converted_id")

viewCoSIAn

Description

viewCoSIAn

Usage

## S4 method for signature 'CoSIAn'
viewCoSIAn(object, slot_name)

Arguments

object

CoSIAn object with all user accessible slots filled
slot_name

name of output slots

Value

slots in CoSIAn object

Examples

Kidney_Genes <- CoSIAn(
    gene_set = c("ENSG00000008710", "ENSG00000152217"),
    i_species = "h_sapiens", input_id = "Ensembl_id",
    o_species = c(
        "d_melanogaster"
    ),
    output_ids = c("Ensembl_id", "Symbol"), mapping_tool = "annotationDBI",
    ortholog_database = "HomoloGene", map_tissues = "heart",
    map_species = c("d_melanogaster"), metric_type = "DS_Gene"
)
viewCoSIAn(Kidney_Genes, "converted_id")