sig2UpDownGmt: Signature(s) files to GMT list; split up and down (inclusive)...

In CoarfaBCM/derecksLabTools: A tool belt for my work at Coarfa lab Baylor College of Medicine

Signature(s) files to GMT list; split up and down (inclusive) based on log2fc

Description

Signature(s) files to GMT list; split up and down (inclusive) based on log2fc

Usage

sig2UpDownGmt(
  signatures_dir,
  pattern = NULL,
  gsub_cols_regex = "EdgeR\\.upperquartile_LRT_RUVr_",
  to_upper = TRUE
)

Arguments

signatures_dir	[type: character] A directory containing signature files.
pattern	[type: character<regex>, default: NULL] A regular expression to match files on read-in.
gsub_cols_regex	[type: character, default: "EdgeR\.upperquartile_LRT_RUVr_"] A regular expression to clean comparison names and thus pathway names.
to_upper	[type: logical, default: TRUE] Convert genes to uppercase; typically yes, lowercase genes are mice type - GSEA works with uppercase humanised genes.

Value

list<character>

CoarfaBCM/derecksLabTools documentation built on April 3, 2022, 10:29 p.m.