facets-internal: facets functions

In mskcc/facets: Cellular Fraction and Copy Numbers from Tumor Sequencing

Description

Internal functions of package facets.

Usage

jointsegsummary(jointseg)
procSnps(rcmat, ndepth=35, het.thresh=0.25, snp.nbhd=250, nX=23,
unmatched=FALSE, ndepthmax=1000)
counts2logROR(out, gbuild, unmatched=FALSE, ugcpct = NULL, f=0.2)
scanSnp(maploc, het, nbhd)
fit.cpt.tree(genomdat, edgelim=10, cval=25, hscl=1, delta=0)
prune.cpt.tree(seg.tree, cval=25)
segsnps(mat, cval=25, hetscale = FALSE, delta=0)
clustersegs(out, jointseg, min.nhet=10)
find.mode(x)
findDiploidLogR(out, cnlr)
km2class(cnlr.med, num.mark)
acnsplit(lr0, lr1, lorsq)
dlrdev(lr2, lr4, out)
fitcncf0(out, dipLogR=0)
optcfutil(tcn, ocn, maf)
mergecf(out)

Details

These are not to be called directly by the user

mskcc/facets documentation built on Oct. 15, 2021, 3:12 p.m.