test_gene_enrichment-methods: analyse gene enrichment with EGSEA

In stemangiola/ttBulk: Brings transcriptomics to the tidyverse

analyse gene enrichment with EGSEA

Description

test_gene_enrichment() takes as input a 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment)) and returns a 'tbl' of gene set information

Usage

test_gene_enrichment(
  .data,
  .formula,
  .sample = NULL,
  .entrez,
  .abundance = NULL,
  contrasts = NULL,
  methods = c("camera", "roast", "safe", "gage", "padog", "globaltest", "ora"),
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease",
    "kegg_metabolism", "kegg_signaling"),
  species,
  cores = 10,
  method = NULL,
  .contrasts = NULL
)

## S4 method for signature 'spec_tbl_df'
test_gene_enrichment(
  .data,
  .formula,
  .sample = NULL,
  .entrez,
  .abundance = NULL,
  contrasts = NULL,
  methods = c("camera", "roast", "safe", "gage", "padog", "globaltest", "ora"),
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease",
    "kegg_metabolism", "kegg_signaling"),
  species,
  cores = 10,
  method = NULL,
  .contrasts = NULL
)

## S4 method for signature 'tbl_df'
test_gene_enrichment(
  .data,
  .formula,
  .sample = NULL,
  .entrez,
  .abundance = NULL,
  contrasts = NULL,
  methods = c("camera", "roast", "safe", "gage", "padog", "globaltest", "ora"),
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease",
    "kegg_metabolism", "kegg_signaling"),
  species,
  cores = 10,
  method = NULL,
  .contrasts = NULL
)

## S4 method for signature 'tidybulk'
test_gene_enrichment(
  .data,
  .formula,
  .sample = NULL,
  .entrez,
  .abundance = NULL,
  contrasts = NULL,
  methods = c("camera", "roast", "safe", "gage", "padog", "globaltest", "ora"),
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease",
    "kegg_metabolism", "kegg_signaling"),
  species,
  cores = 10,
  method = NULL,
  .contrasts = NULL
)

## S4 method for signature 'SummarizedExperiment'
test_gene_enrichment(
  .data,
  .formula,
  .sample = NULL,
  .entrez,
  .abundance = NULL,
  contrasts = NULL,
  methods = c("camera", "roast", "safe", "gage", "padog", "globaltest", "ora"),
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease",
    "kegg_metabolism", "kegg_signaling"),
  species,
  cores = 10,
  method = NULL,
  .contrasts = NULL
)

## S4 method for signature 'RangedSummarizedExperiment'
test_gene_enrichment(
  .data,
  .formula,
  .sample = NULL,
  .entrez,
  .abundance = NULL,
  contrasts = NULL,
  methods = c("camera", "roast", "safe", "gage", "padog", "globaltest", "ora"),
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease",
    "kegg_metabolism", "kegg_signaling"),
  species,
  cores = 10,
  method = NULL,
  .contrasts = NULL
)

Arguments

.data	A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment))
.formula	A formula with no response variable, representing the desired linear model
.sample	The name of the sample column
.entrez	The ENTREZ ID of the transcripts/genes
.abundance	The name of the transcript/gene abundance column
contrasts	This parameter takes the format of the contrast parameter of the method of choice. For edgeR and limma-voom is a character vector. For DESeq2 is a list including a character vector of length three. The first covariate is the one the model is tested against (e.g., ~ factor_of_interest)
methods	A character vector. One or 3 or more methods to use in the testing (currently EGSEA errors if 2 are used). Type EGSEA::egsea.base() to see the supported GSE methods.
gene_sets	A character vector or a list. It can take one or more of the following built-in collections as a character vector: c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"), to be used with EGSEA buildIdx. c1 is human specific. Alternatively, a list of user-supplied gene sets can be provided, to be used with EGSEA buildCustomIdx. In that case, each gene set is a character vector of Entrez IDs and the names of the list are the gene set names.
species	A character. It can be human, mouse or rat.
cores	An integer. The number of cores available
method	DEPRECATED. Please use methods.
.contrasts	DEPRECATED - This parameter takes the format of the contrast parameter of the method of choice. For edgeR and limma-voom is a character vector. For DESeq2 is a list including a character vector of length three. The first covariate is the one the model is tested against (e.g., ~ factor_of_interest)

Details

'r lifecycle::badge("maturing")'

This wrapper executes ensemble gene enrichment analyses of the dataset using EGSEA (DOI:0.12688/f1000research.12544.1)

dge = data |> keep_abundant( factor_of_interest = !!as.symbol(parse_formula(.formula)[[1]]), !!.sample, !!.entrez, !!.abundance )

# Make sure transcript names are adjacent [...] as_matrix(rownames = !!.entrez) edgeR::DGEList(counts = .)

idx = buildIdx(entrezIDs = rownames(dge), species = species, msigdb.gsets = msigdb.gsets, kegg.exclude = kegg.exclude)

dge |>

# Calculate weights limma::voom(design, plot = FALSE) |>

# Execute EGSEA egsea( contrasts = my_contrasts, baseGSEAs = methods, gs.annots = idx, sort.by = "med.rank", num.threads = cores, report = FALSE )

Value

A consistent object (to the input)

A consistent object (to the input)

A consistent object (to the input)

A consistent object (to the input)

A consistent object (to the input)

A consistent object (to the input)

Examples

## Not run: 

library(SummarizedExperiment)
se = tidybulk::se_mini
rowData( se)$entrez = rownames(se )
df_entrez = aggregate_duplicates(se,.transcript = entrez )

library("EGSEA")

	test_gene_enrichment(
		df_entrez,
		~ condition,
		.sample = sample,
		.entrez = entrez,
		.abundance = count,
         methods = c("roast" , "safe", "gage"  ,  "padog" , "globaltest", "ora" ),
         gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "kegg_disease", "kegg_metabolism", "kegg_signaling"),
		species="human",
		cores = 2
	)


## End(Not run)

stemangiola/ttBulk documentation built on Dec. 14, 2024, 6:12 a.m.