R: Missing genotype percentage

seqMissing {SeqArray}

R Documentation

Missing genotype percentage

Description

Calculates the missing rates per variant or per sample.

Usage

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

Arguments

`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`	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.

Value

A vector of missing rates, or a list(variant, sample) for both variants and samples.

Author(s)

Xiuwen Zheng

Examples

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

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

summary(m1 <- seqMissing(f, TRUE, .progress=TRUE))
summary(m2 <- seqMissing(f, FALSE, .progress=TRUE))

str(m <- seqMissing(f, NA, .progress=TRUE))
identical(m1, m$variant)  # should be TRUE
identical(m2, m$sample)   # should be TRUE

# close the GDS file
seqClose(f)

[Package SeqArray version 1.27.15 Index]