getMAF: Obtain minor allele frequencies per SNP or per sample

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

Obtain minor allele frequencies per SNP or per sample

Description

Obtain minor allele frequencies per SNP or per sample

Usage

getMAF(object, target = "marker", valid = TRUE, ...)

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

Arguments

object	A GbsrGenotypeData object.
target	Either of "marker" and "sample".
valid	A logical value. See details.
...	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 the minor allele frequencies 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)

getMAF(gds)

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

tomoyukif/GBScleanR documentation built on March 12, 2024, 6:27 a.m.