getSDReadRef: Obtain standard deviations of total reference read counts per...

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

Obtain standard deviations of total reference read counts per SNP or per sample

Description

Obtain standard deviations of total reference read counts per SNP or per sample

Usage

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

## S4 method for signature 'GbsrGenotypeData'
getSDReadRef(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 summary statistics to 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 standard deviations of reference 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)

getSDReadRef(gds)

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

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