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Make a PathScore input file from MAF data

Source: R/make_PathScore_input.R
make_PathScore_input.Rd

Produce a file from MAF data for use with PathScore, a web tool for identifying significantly altered pathways in cancer. See https://pathscore.publichealth.yale.edu/ and https://doi.org/10.1093/bioinformatics/btw512.

Usage

make_PathScore_input(maf, file = NULL, genome = "hg38")

Arguments

maf

An MAF-like data.table, as from preload_maf(). If the MAF has a column named annot, this column will be preserved in output (since PathScore supports an optional annotation column with this name).

file

Name/path where PathScore-formatted data should be written. Will be a tab-delimited text file.

genome

The genome build associated with the MAF file. Must be "hg38" (default) or "hg19".

Value

A copy of the PathScore-formatted data as a data.table.