In pneuvial/c3co: Cancer Cell Clonality using Copy-Number

Introduction

This document provides a brief tutorial for using the c3co package on data segmented by PSCBS (@olshen11parent-specific).

library("c3co")
library("c3co.data")

Using wrapper

In this document we run c3co on a public data set in the PSCBS format, which has been saved into the c3co.data package. The PSCBSwrapper() function segments and saves data from PSCBS format to c3co format.

data("PSCBSdata", package = "c3co.data")
segDat <- PSCBSwrapper(PSCBSdata, stat = "C1C2")

Run c3co

Now, you can run c3co by using this line:

lambda.grid <- seq(from = 1e-4, to = 1e-3, length.out = 10L)
parameters.grid <- list(lambda = lambda.grid, nb.arch = 2:5)
resc3co <- c3co(dat = NULL, parameters.grid, segDat = segDat)

pvePlot(resc3co)

Wplot(resc3co, idxBest = 3L)

df <- createZdf(resc3co, chromosomes = 1:2, idxBest = 2)

Zplot(df, scalePosToMb = TRUE)

Session Information

sessionInfo()

References

pneuvial/c3co documentation built on May 25, 2019, 10:21 a.m.