Missing genotype percentage (original) (raw)
seqMissing: Missing genotype percentage
Description Usage Arguments Details Value Author(s) See Also Examples
Calculates the missing rates per variant or per sample.
| 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, seeseqParallel 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](/bioc/SeqArray/man/seqAlleleFreq.html), [seqNumAllele](/bioc/SeqArray/man/seqNumAllele.html),[seqParallel](/bioc/SeqArray/man/seqParallel.html), [seqGetParallel](/bioc/SeqArray/man/seqGetParallel.html)
SeqArray documentation built on Nov. 8, 2020, 5:08 p.m.