getCountRead: Obtain total read counts per SNP or per sample

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

Obtain total read counts per SNP or per sample

Description

Obtain total read counts per SNP or per sample

Usage

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

## S4 method for signature 'GbsrGenotypeData'
getCountRead(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 countRead() 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 integer vector of total read counts (reference allele reads + alternative allele reads) 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)
gds <- countRead(gds)

getCountRead(gds)

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

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