facets2n-internal: facets functions

In rptashkin/facets2n: Cellular Faction and Copy Numbers from Tumor Sequencing

facets functions

Description

Internal functions of package facets2n.

Usage

jointsegsummary(jointseg)
procSnps(rcmat, ndepth=35, het.thresh=0.25, snp.nbhd=250, gbuild="hg19",
unmatched=FALSE, ndepthmax=5000, donorCounts = NULL)
counts2logROR(mat, gbuild, unmatched=FALSE, MandUnormal = FALSE, f, spanT, spanA, spanX)
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)
onepass(x, trace, unif, rho, rhov, prior, posterior, sigma, min.nhet, rho.clust, maxiter, eps)
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

rptashkin/facets2n documentation built on May 11, 2022, 1:34 p.m.