getCountAlleleAlt: Obtain total alternative allele counts per SNP or per sample

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

Obtain total alternative allele counts per SNP or per sample

Description

Obtain total alternative allele counts per SNP or per sample

Usage

getCountAlleleAlt(object, target = "marker", valid = TRUE, prop = FALSE, ...)

## S4 method for signature 'GbsrGenotypeData'
getCountAlleleAlt(object, target, valid, prop)

Arguments

object	A GbsrGenotypeData object.
target	Either of "marker" and "sample".
valid	A logical value. See details.
prop	A logical value whether to return values as proportions of total alternative allele counts to total non missing allele counts or not.
...	Unused.

Details

You need to execute countGenotype() to calculate sumaary statisticsto be obtained via this function. If valid = TRUE, the chromosome information of markers which are labeled TRUE in the sample slot will be returned. validMar() tells you which samples are valid.

Value

A numeric vector of (proportion of) alternative alleles per marker.

Examples

gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)
gds <- countGenotype(gds)
getCountAlleleAlt(gds)
closeGDS(gds) # Close the connection to the GDS file

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.