resetSamFilter: Reset the filter made by 'setSamFilter()'

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

Reset the filter made by setSamFilter()

Description

Remove "invalid" labels put on samples and make all samples valid.

Usage

resetSamFilter(object, ...)

## S4 method for signature 'GbsrGenotypeData'
resetSamFilter(object)

Arguments

object	A GbsrGenotypeData object.
...	Unused.

Value

A GbsrGenotypeData object after removing all filters on samples.

Examples

# Create a GDS file from a sample VCF file.
vcf_fn <- system.file("extdata", "sample.vcf", package = "GBScleanR")
gds_fn <- tempfile("sample", fileext = ".gds")
gbsrVCF2GDS(vcf_fn = vcf_fn, out_fn = gds_fn, force = TRUE)

# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds <- loadGDS(gds_fn)

# Summarize the information needed for filtering.
gds <- countGenotype(gds)
gds <- countRead(gds)

gds <- setSamFilter(gds,
                       id = getSamID(gds)[1:10],
                       missing = 0.2,
                       dp = c(5, Inf))

# Reset all filters applied above.
gds <- resetSamFilter(gds)

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

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.