applyMethod: Apply method to GDS object

In smgogarten/SeqVarTools: Tools for variant data

Apply method to GDS object

Description

Apply a method to a subset of variants and/or samples in a GDS object

Usage

## S4 method for signature 'SeqVarGDSClass,function,character'
applyMethod(gdsobj, FUN, variant, sample=NULL, ...)
## S4 method for signature 'SeqVarGDSClass,function,numeric'
applyMethod(gdsobj, FUN, variant, sample=NULL, ...)
## S4 method for signature 'SeqVarGDSClass,function,GRanges'
applyMethod(gdsobj, FUN, variant, sample=NULL, ...)
## S4 method for signature 'SeqVarGDSClass,function,missing'
applyMethod(gdsobj, FUN, variant, sample=NULL, ...)

Arguments

gdsobj	A SeqVarGDSClass object with VCF data.
FUN	A method or function to be applied to gdsobj.
variant	A vector of variant.id values or a GRanges object defining the variants to be included in the call to FUN.
sample	A vector of sample.id values defining the samples to be included in the call to FUN.
...	Additional arguments, passed to FUN.

Details

applyMethod applies a method or function FUN to the subset of variants defined by variant and samples defined by sample in a GDS object.

If a filter was previously set with seqSetFilter, it will be saved and reset after the call to applyMethod.

Value

The result of the call to FUN.

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass

Examples

gds <- seqOpen(seqExampleFileName("gds"))
variant.id <- seqGetData(gds, "variant.id")
sample.id <- seqGetData(gds, "sample.id")
applyMethod(gds, getGenotype, variant.id[1:5], sample.id[1:10])

library(GenomicRanges)
chrom <- seqGetData(gds, "chromosome")
pos22 <- seqGetData(gds, "position")[chrom == 22]
ranges <- GRanges(seqnames="22", IRanges(min(pos22), max(pos22)))
applyMethod(gds, heterozygosity, ranges, margin="by.sample")
applyMethod(gds, heterozygosity, ranges, margin="by.variant")

seqClose(gds)

smgogarten/SeqVarTools documentation built on Sept. 15, 2024, 1:08 p.m.