test_gene_enrichment_bulk_EGSEA {tidybulk}R Documentation

Get gene enrichment analyses using EGSEA

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


[Package tidybulk version 1.2.1 Index]