test_gene_overrepresentation-methods: analyse gene over-representation with GSEA

In tidybulk: Brings transcriptomics to the tidyverse

Description

test_gene_overrepresentation() takes as input a 'tbl' formatted as | <SAMPLE> | <ENSEMBL_ID> | <COUNT> | <...> | and returns a 'tbl' with the GSEA statistics

Usage

test_gene_overrepresentation(
  .data,
  .sample = NULL,
  .entrez,
  .do_test,
  species,
  gene_set = NULL
)

## S4 method for signature 'spec_tbl_df'
test_gene_overrepresentation(
  .data,
  .sample = NULL,
  .entrez,
  .do_test,
  species,
  gene_set = NULL
)

## S4 method for signature 'tbl_df'
test_gene_overrepresentation(
  .data,
  .sample = NULL,
  .entrez,
  .do_test,
  species,
  gene_set = NULL
)

## S4 method for signature 'tidybulk'
test_gene_overrepresentation(
  .data,
  .sample = NULL,
  .entrez,
  .do_test,
  species,
  gene_set = NULL
)

Arguments

.data	A 'tbl' formatted as | <SAMPLE> | <TRANSCRIPT> | <COUNT> | <...> |
.sample	The name of the sample column
.entrez	The ENTREZ ID of the transcripts/genes
.do_test	A boolean column name symbol. It indicates the transcript to check
species	A character. For example, human or mouse. MSigDB uses the latin species names (e.g., \"Mus musculus\", \"Homo sapiens\")
gene_set	A character vector. The subset of MSigDB datasets you want to test against (e.g. \"C2\"). If NULL all gene sets are used (suggested). This argument was added to avoid time overflow of the examples.

Details

\lifecycle

maturing

This wrapper execute gene enrichment analyses of the dataset using a list of transcripts and GSEA. This wrapper uses clusterProfiler (DOI: doi.org/10.1089/omi.2011.0118) on the back-end.

Undelying method: msigdbr::msigdbr(species = species) nest(data = -gs_cat) mutate(test = map( data, ~ clusterProfiler::enricher( my_entrez_rank, TERM2GENE=.x pvalueCutoff = 1 ) ))

Value

A 'tbl' object

A 'tbl' object

A 'tbl' object

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)
df_entrez = mutate(df_entrez, do_test = transcript %in% c("TNFRSF4", "PLCH2", "PADI4", "PAX7"))

	test_gene_overrepresentation(
		df_entrez,
		.sample = sample,
		.entrez = entrez,
		.do_test = do_test,
		species="Homo sapiens",
   gene_set=c("C2")
	)

tidybulk documentation built on April 7, 2021, 6 p.m.