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,
  methods,
  gene_sets,
  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)

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

Value

A tibble with edgeR results


[Package tidybulk version 1.4.0 Index]