facets2n-internal | R Documentation |
Internal functions of package facets2n.
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)
These are not to be called directly by the user
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