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

View source: R/Methods.R

Description

Calculates the missing rates per variant or per sample.

Usage

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

Arguments

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

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# 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)