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

Maturing lifecycle

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]