getMedianReadRef: Obtain quantile values of total reference read counts per SNP...

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

Obtain quantile values of total reference read counts per SNP or per sample

Description

Obtain quantile values of total reference read counts per SNP or per sample

Usage

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

## S4 method for signature 'GbsrGenotypeData'
getMedianReadRef(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 numeric vector of the quantile values of 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)

# Calculate means, standard deviations, quantiles of read counts
# per marker and per sample with or without standardization of
# the counts and store them in the [marker] and [sample] slots
# of the [GbsrGenotypeData] object.
gds <- countRead(gds)

getMedianReadRef(gds)

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

tomoyukif/GBScleanR documentation built on April 27, 2024, 9:06 a.m.