make_PathScore_input: Make a PathScore input file from MAF data

In Townsend-Lab-Yale/cancereffectsizeR: Calculate Cancer Effect Size

Make a PathScore input file from MAF data

Description

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.

Townsend-Lab-Yale/cancereffectsizeR documentation built on April 28, 2024, 6:14 p.m.