GenerateGSEA: Create a rnk file for Gene Set Enrichment Analysis

In kevincjnixon/BinfTools: Useful functions for standard analyses

Create a rnk file for Gene Set Enrichment Analysis

Description

This function creates a ranked list of genes for use with a PreRanked Gene Set Enrichment Analysis (GSEA) (www.gsea-msigdb.org/gsea)

Usage

GenerateGSEA(
  res,
  filename = "GSEA.rnk",
  bystat = TRUE,
  byFC = FALSE,
  plotRNK = TRUE,
  retRNK = FALSE
)

Arguments

res	A DESeq2 results object obtained from 'results(dds)' or a data.frame with the same column name values as a DESeq2 results object and rownames as genes
filename	Path to the output .rnk file. Default is "./GSEA.rnk". Set NULL to not write out to file.
bystat	Boolean values determining if genes should be ranked by column 'stat'. If TRUE, and no column 'stat', genes will be ranked using the -log10 of column 'pvalue'. Default is TRUE.
byFC	Boolean values determining if genes should be ranked by column 'log2FoldChange'Default is FALSE.
plotRNK	Boolean indicating if ranked scores should be plotted. Default=TRUE
retRNK	Boolean indicating if ranked list should be returned as data frame object

Value

Exports a ranked gene list. If both bystat and byFC are true, ranking will be abs(stat)*log2FoldChange.

kevincjnixon/BinfTools documentation built on July 10, 2024, 11:46 a.m.