seqMissing {SeqArray} | R Documentation |
Calculates the missing rates per variant or per sample.
seqMissing(gdsfile, per.variant=TRUE, .progress=FALSE, parallel=seqGetParallel(), verbose=FALSE)
gdsfile |
a |
per.variant |
missing rate per variant if |
.progress |
[deprecated] if TRUE, show progress information |
parallel |
|
verbose |
if |
If the gds node 'genotype/data' (integer genotypes) is not available, the node 'annotation/format/DS' (numeric genotype dosages for alternative alleles) will be used to calculate allele frequencies. At a site, it assumes 'annotation/format/DS' stores the dosage of the 1st alternative allele in the 1st column, 2nd alt. allele in the 2nd column if it is multi-allelic, and so on.
A vector of missing rates, or a list(variant, sample)
for both
variants and samples.
Xiuwen Zheng
seqAlleleFreq
, seqNumAllele
,
seqParallel
, seqGetParallel
# the GDS file (gds.fn <- seqExampleFileName("gds")) # display (f <- seqOpen(gds.fn)) summary(m1 <- seqMissing(f, TRUE, verbose=TRUE)) summary(m2 <- seqMissing(f, FALSE, verbose=TRUE)) str(m <- seqMissing(f, NA, verbose=TRUE)) identical(m1, m$variant) # should be TRUE identical(m2, m$sample) # should be TRUE # close the GDS file seqClose(f)