procXSnps: Takes a snp-pileup file and determines sex of sample and any...

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

Takes a snp-pileup file and determines sex of sample and any unmatched normals based on number of chrX het SNPs, as males should not have het X

Description

Takes a snp-pileup file and determines sex of sample and any unmatched normals based on number of chrX het SNPs, as males should not have het X

Usage

procXSnps(
  pileup,
  ndepth = 35,
  het.thresh = 0.25,
  snp.nbhd = 250,
  gbuild = "hg19",
  unmatched = FALSE,
  ndepthmax = 5000,
  phet = 0.01
)

Arguments

pileup	(character) A snp-pileup generated pileup file that has been analyzed with readSnpMatrix(). Expect columns "Chromosome", "Position", "NOR.DP", "NOR.RD", "TUM.DP", and "TUM.RD". Can be a pileup file that has been merged with common loci of reference normals processed with PreProcSnpPileup()
ndepth	(numeric) minimum normal sample depth to keep
het.thresh	(numeric) vaf threshold to call a SNP heterozygous
snp.nbhd	(logical) window size
gbuild	(character) genome build version.
unmatched	(logical)
ndepthmax	(numeric) loci for which normal coverage exceeds this number (default is 5000) will be discarded as PCR duplicates. Fof high coverage sample increase this and ndepth commensurately.
phet	(numeric) proportion heterzygous chrX SNPs to classify sample as Female

Value

output a table of samples analyzed and imputed sex.

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