prepareGSEAgenesets: Prepare GSEA gene sets

In nuno-agostinho/cTRAP: Identification of candidate causal perturbations from differential gene expression data

Prepare GSEA gene sets

Description

Prepare GSEA gene sets

Usage

prepareGSEAgenesets(input, geneSize)

Arguments

input	Named numeric vector of differentially expressed genes whose names are gene identifiers and respective values are a statistic that represents significance and magnitude of differentially expressed genes (e.g. t-statistics); or character of gene symbols composing a gene set that is tested for enrichment in reference data (only used if method includes gsea)
geneSize	Numeric: number of top up-/down-regulated genes to use as gene sets to test for enrichment in reference data; if a 2-length numeric vector, the first index is the number of top up-regulated genes and the second index is the number of down-regulated genes used to create gene sets; only used if method includes gsea and if input is not a gene set

Value

List of gene sets

nuno-agostinho/cTRAP documentation built on March 28, 2024, 3:59 p.m.