MutSig: 'MutSig' plot mutational signature activity of given...

In xindizhang/SigAct: A package for tracking mutational signatures over time

Description

MutSig takes three input file (a .csv file of signature activities corrdinate where x is the esudotime and y is the signature activity, a .txt file of signaficant signature activity change point, and a .txt file for the pesudo-timeline) and generates a plot of a pesudotime (extimated by mutant allel per cell) vs. signature activities for single sample. For two two chronological samples, it takes six input file and generate the plot. This function is inspired by TrackSig. Please see reference at the top of this file

Usage

MutSig(sigActPoints, changepoints, phis, sigActPoints2 = NULL,
  changepoints2 = NULL, phis2 = NULL)

Arguments

sigActPoints	absolute path of a CSV file of signature activities across pesudotime for each signature
changepoints	absolute path of a txt file containing the significant changepoints of signature activities
phis	absolute path of txt containing the pesudo-timeline
sigActPoints2	an optional file for two seamples plot. See sigActPoints for the formate
changepoints2	an optional file for two seamples plot. See changepoint for the formate
phis2	an optional file for two seamples plot. See phis for the formate

Value

a list containg a pesudotime (estimated by number of mutants per cancer cell) vs.signature activity plot and signatures. For two chronological samples, it returns list containg above information for each sample

Examples

# For single sample
sigActPoints <- system.file("extdata", "sigActPoints.csv", package = "SigAct")
changepoints <- system.file("extdata", "changepoints.txt", package = "SigAct")
phis <- system.file("extdata", "phis.txt", package = "SigAct")
MutSig(sigActPoints, changepoints, phis)
# For two samples
sigActPoints2 <- system.file("extdata", "sigActPoints2.csv", package = "SigAct")
changepoints2 <- system.file("extdata", "changepoints2.txt", package = "SigAct")
phis2 <- system.file("extdata", "phis2.txt", package = "SigAct")
MutSig(sigActPoints, changepoints, phis, sigActPoints2, changepoints2, phis2)

xindizhang/SigAct documentation built on May 30, 2019, 11:47 p.m.