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]