View source: R/facets-procreads.R
procXSnps | R Documentation |
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
procXSnps( pileup, ndepth = 35, het.thresh = 0.25, snp.nbhd = 250, gbuild = "hg19", unmatched = FALSE, ndepthmax = 5000, phet = 0.01 )
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 |
output a table of samples analyzed and imputed sex.
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