test_gene_enrichment {tidybulk} | R Documentation

## analyse gene enrichment with EGSEA

### Description

test_gene_enrichment() takes as imput a 'tbl' formatted as | <SAMPLE> | <ENSEMBL_ID> | <COUNT> | <...> | and returns a 'tbl' with the additional transcript symbol column

### Usage

    test_gene_enrichment(
      .data,
      .formula,
      .sample = NULL,
      .entrez,
      .abundance = NULL,
      .contrasts = NULL,
      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 doce of the transcripts/genes
`.abundance` | The name of the transcript/gene abundance column
`.contrasts` | = NULL,
`species` | A character. For example, human or mouse
`cores` | An integer. The number of cores available

### Details

This wrapper execute gene enrichment analyses of the dataset

### Value

A 'tbl' object

### Examples

    df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcript = transcript, .sample = sample)
    df_entrez = aggregate_duplicates(df_entrez, aggregation_function = sum, .sample = sample, .transcript = entrez, .abundance = count)

    library("EGSEA")

    	test_gene_enrichment(
    		df_entrez,
    		~ condition,
    		.sample = sample,
    		.entrez = entrez,
    		.abundance = count,
    		species="human"
    	)

[Package tidybulk version 0.99.23 Index]