resetFilter: Reset all filters made by 'setSamFilter()', 'setMarFilter()',...

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

Reset all filters made by setSamFilter(), setMarFilter(), and setCallFilter().

Description

Return all data intact.

Usage

resetFilter(object, ...)

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

Arguments

object	A GbsrGenotypeData object.
...	Unused.

Value

A GbsrGenotypeData object after removing all filters.

A GbsrGenotypeData object after removing all filters on markers.

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)

# `setCallFilter()` do not require summarized information of
# genotype counts and read counts.
gds <- setCallFilter(gds, dp_count = c(5, Inf))

# `setSamFilter()` and `setMarFilter()` needs information of
# the genotype count summary and the read count summary.
gds <- countGenotype(gds)
gds <- countRead(gds)

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

gds <- setMarFilter(gds,
                      id = getMarID(gds)[1:100],
                      missing = 0.2,
                      dp = c(5, Inf))

gds <- setInfoFilter(gds, mq = 40, qd = 20)

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

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

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