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(), verbose=FALSE)

### 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` | [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

### Details

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.

### Value

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

### Author(s)

Xiuwen Zheng

### See Also

`seqAlleleFreq`, `seqNumAllele`, `seqParallel`, `seqGetParallel`

### Examples

    # 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)

[Package SeqArray version 1.30.0 Index]