missingGenotypeRate {SeqVarTools} | R Documentation |
Calculate missing genotype rate by variant or by sample
## S4 method for signature 'SeqVarGDSClass' missingGenotypeRate(gdsobj, margin=c("by.variant", "by.sample"), use.names=FALSE, parallel=FALSE)
gdsobj |
A |
margin |
Possible values are "by.variant" or "by.sample," indicating whether the calculation should be done over all samples for each variant, or over all variants for each sample. |
use.names |
A logical indicating whether to assign variant IDs as names of the output vector. |
parallel |
Logical, numeric, or other value to control parallel
processing; see |
Calculates the fraction of missing genotypes in a GDS object, either by variant or by sample.
A numeric vector of missing genotype rates. If
margin="by.variant"
, the vector will have length equal to the
number of variants in the GDS object. If margin="by.sample"
,
the vector will have length equal to the number of samples.
Stephanie Gogarten
SeqVarGDSClass
,
applyMethod
,
getGenotype
gds <- seqOpen(seqExampleFileName("gds")) head(missingGenotypeRate(gds, margin="by.variant")) head(missingGenotypeRate(gds, margin="by.sample")) seqClose(gds)