write_gsea_rnk: Write DESeq results to GSEA rank file

In HuntsmanCancerInstitute/hciR: RNA-seq workflows at HCI

Write DESeq results to GSEA rank file

Description

Writes gene name (or human homolog) and log2 fold change sorted in descending order to a list of vectors or tab-delimited file. Duplicate gene name with the lowest absolute fold change are removed.

Usage

write_gsea_rnk(
  res,
  write = TRUE,
  protein_coding = TRUE,
  na_pvalue = FALSE,
  run,
  filename = FALSE
)

Arguments

res	a list of DESeq results
write	write a file (default) or return a list of named vectors
protein_coding	only write protein_coding genes
na_pvalue	remove genes with NA p-values (extreme count outliers and low mean normalized counts flagged by independent filtering step)
run	add run ID to file name
filename	name for output file, strig, e.g. "treatment_vs_control.rnk"

Value

Tab-delimited file with gene name and log2 fold change

Author(s)

Chris Stubben

Examples

## Not run: 
  write_gsea_rnk(res)

## End(Not run)

HuntsmanCancerInstitute/hciR documentation built on March 26, 2024, 3:09 a.m.