SeqArray (version 1.12.5)

seqMissing: Missing genotype percentage

Description

Calculates the missing rates per variant or per sample.

Usage

seqMissing(gdsfile, per.variant=TRUE, .progress=FALSE, parallel=getOption("seqarray.parallel", FALSE))

Arguments

gdsfile

a SeqVarGDSClass object

per.variant

missing rate per variant if TRUE, or missing rate per sample if FALSE

.progress

if TRUE, show progress information

parallel

FALSE (serial processing), TRUE (parallel processing) or other value; parallel is passed to the argument cl in seqParallel, see seqParallel for more details.

Value

A vector of missing rates.

See Also

seqAlleleFreq, seqNumAllele, seqParallel

Examples

# the GDS file
(gds.fn <- seqExampleFileName("gds"))

# display
(f <- seqOpen(gds.fn))

summary(seqMissing(f, TRUE, .progress=TRUE))

summary(seqMissing(f, FALSE, .progress=TRUE))

# close the GDS file
seqClose(f)