gsea.results: Get GSEA results

In FerrenaAlexander/FerrenaBulkRNAseq: Pipeline for analysis of bulkRNAseq data

Get GSEA results

Description

Using FGSEA, DESeq2 results, and input pathways, compute GSEA results.

Usage

gsea.results(results, pathways = NULL, weightmethod = NULL, onlypos = NULL)

Arguments

results	dataframe with column names similar to the output of DESeq2::results() function, with columns labeleld "log2FoldChange" and "pvalue"
pathways	list of character vectors containing gene names in same format as results; each list element's name should be the name of the pathway
weightmethod	one of "pvalue" or "foldchange". how to weight the results results. Default is "pvalue"
onlypos	T/F. whether to use only positive log fold change genes. Default is False.

Value

a list with two elements; 1, a dataframe with FGSEA results; 2, a list of character vectors showing the leading edge genes for each pathway

FerrenaAlexander/FerrenaBulkRNAseq documentation built on Oct. 16, 2022, 8:18 a.m.