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