getCountGenoRef: Obtain total reference genotype counts per SNP or per sample

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

Obtain total reference genotype counts per SNP or per sample

Description

Obtain total reference genotype counts per SNP or per sample

Usage

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

## S4 method for signature 'GbsrGenotypeData'
getCountGenoRef(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 reference genotype counts to total non missing genotype 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) homozygous reference genotype calls per marker.

Examples

# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)

# Summarize the genotype count information and store them in the
# [marker] and [sample] slots of the [GbsrGenotypeData] object.
gds <- countGenotype(gds)

getCountGenoRef(gds)

# Close the connection to the GDS file.
closeGDS(gds)

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