test_gene_enrichment_bulk_EGSEA: Get gene enrichment analyses using EGSEA

In tidybulk: Brings transcriptomics to the tidyverse

Description

Get gene enrichment analyses using EGSEA

Usage

test_gene_enrichment_bulk_EGSEA(
  .data,
  .formula,
  .sample = NULL,
  .entrez,
  .abundance = NULL,
  .contrasts = NULL,
  method,
  species,
  cores = 10
)

Arguments

.data	A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
.formula	A formula with no response variable, representing the desired linear model
.sample	The name of the sample column
.entrez	The ENTREZ code of the transcripts/genes
.abundance	The name of the transcript/gene abundance column
.contrasts	A character vector. See edgeR makeContrasts specification for the parameter 'contrasts'. If contrasts are not present the first covariate is the one the model is tested against (e.g., ~ factor_of_interest)
method	A character vector. The methods to be included in the ensembl. Type EGSEA::egsea.base() to see the supported GSE methods.
species	A character. For example, human or mouse
cores	An integer. The number of cores available

Value

A tibble with edgeR results

tidybulk documentation built on April 7, 2021, 6 p.m.