test_gene_rank-methods: analyse gene rank with GSEA

In stemangiola/tidyBulk: Brings transcriptomics to the tidyverse

analyse gene rank with GSEA

Description

test_gene_rank() takes as input a 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment)) and returns a 'tbl' with the GSEA statistics

Usage

test_gene_rank(
  .data,
  .entrez,
  .arrange_desc,
  species,
  .sample = NULL,
  gene_sets = NULL,
  gene_set = NULL
)

## S4 method for signature 'spec_tbl_df'
test_gene_rank(
  .data,
  .entrez,
  .arrange_desc,
  species,
  .sample = NULL,
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7"),
  gene_set = NULL
)

## S4 method for signature 'tbl_df'
test_gene_rank(
  .data,
  .entrez,
  .arrange_desc,
  species,
  .sample = NULL,
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7"),
  gene_set = NULL
)

## S4 method for signature 'tidybulk'
test_gene_rank(
  .data,
  .entrez,
  .arrange_desc,
  species,
  .sample = NULL,
  gene_sets = c("h", "c1", "c2", "c3", "c4", "c5", "c6", "c7"),
  gene_set = NULL
)

## S4 method for signature 'SummarizedExperiment'
test_gene_rank(
  .data,
  .entrez,
  .arrange_desc,
  species,
  .sample = NULL,
  gene_sets = NULL,
  gene_set = NULL
)

## S4 method for signature 'RangedSummarizedExperiment'
test_gene_rank(
  .data,
  .entrez,
  .arrange_desc,
  species,
  .sample = NULL,
  gene_sets = NULL,
  gene_set = NULL
)

Arguments

.data	A 'tbl' (with at least three columns for sample, feature and transcript abundance) or 'SummarizedExperiment' (more convenient if abstracted to tibble with library(tidySummarizedExperiment))
.entrez	The ENTREZ ID of the transcripts/genes
.arrange_desc	A column name of the column to arrange in decreasing order
species	A character. For example, human or mouse. MSigDB uses the latin species names (e.g., \"Mus musculus\", \"Homo sapiens\")
.sample	The name of the sample column
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.
gene_set	DEPRECATED. Use gene_sets instead.

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: # Get gene sets signatures msigdbr::msigdbr(species = species)

# Filter specific gene_sets if specified. This was introduced to speed up examples executionS when( !is.null(gene_sets ) ~ filter(., gs_cat ~ (.) ) |>

# Execute calculation nest(data = -gs_cat) |> mutate(fit = map( data, ~ clusterProfiler::GSEA( my_entrez_rank, TERM2GENE=.x |> select(gs_name, entrez_gene), pvalueCutoff = 1 )

))

Value

A consistent object (to the input)

A 'spec_tbl_df' object

A 'tbl_df' object

A 'tidybulk' object

A 'SummarizedExperiment' object

A 'RangedSummarizedExperiment' object

Examples

print("Not run for build time.")

## Not run: 

df_entrez = tidybulk::se_mini
df_entrez = mutate(df_entrez, do_test = .feature %in% c("TNFRSF4", "PLCH2", "PADI4", "PAX7"))
df_entrez  = df_entrez |> test_differential_abundance(~ condition)


test_gene_rank(
	df_entrez,
		.sample = .sample,
	.entrez = entrez,
		species="Homo sapiens",
   gene_sets =c("C2"),
 .arrange_desc = logFC
	)

## End(Not run)

stemangiola/tidyBulk documentation built on Oct. 22, 2024, 5:19 a.m.