getMeanReadRef: Obtain mean values of total reference read counts per SNP or...

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

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

Description

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

Usage

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

## S4 method for signature 'GbsrGenotypeData'
getMeanReadRef(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 mean values of reference allele reads per marker.

Examples

gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)
gds <- countRead(gds)
getMeanReadRef(gds)
closeGDS(gds) # Close the connection to the GDS file

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