gmt_to_list {clustifyr} | R Documentation |
convert gmt format of pathways to list of vectors
gmt_to_list( path, cutoff = 0, sep = "\thttp://www.broadinstitute.org/gsea/msigdb/cards/.*?\t" )
path |
gmt file path |
cutoff |
remove pathways with less genes than this cutoff |
sep |
sep used in file to split path and genes |
list of genes in each pathway
gmt_file <- system.file( "extdata", "c2.cp.reactome.v6.2.symbols.gmt.gz", package = "clustifyr" ) gl <- gmt_to_list(path = gmt_file) length(gl)