seqMissing: Missing genotype percentage
In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description Usage Arguments Details Value Author(s) See Also Examples

Calculates the missing rates per variant or per sample.

1 2	seqMissing(gdsfile, per.variant=TRUE, .progress=FALSE, parallel=seqGetParallel(), verbose=FALSE)

`gdsfile`	a `SeqVarGDSClass` object
`per.variant`	missing rate per variant if `TRUE`, missing rate per sample if `FALSE`, or calculating missing rates for variants and samples if `NA`
`.progress`	[deprecated] if TRUE, show progress information
`parallel`	`FALSE` (serial processing), `TRUE` (multicore processing), numeric value or other value; `parallel` is passed to the argument `cl` in `seqParallel`, see `seqParallel` for more details.
`verbose`	if `TRUE`, show progress information

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)