resetMarFilter: Reset the filter made by 'setMarFilter()'

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

Reset the filter made by setMarFilter()

Description

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

Usage

resetMarFilter(object, ...)

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

Arguments

object	A GbsrGenotypeData object.
...	Unused.

Value

A GbsrGenotypeData object after removing all filters on markers.

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)

# Check the number of markers.
nmar(gds)

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

# filter out some markers meeting the criteria.
gds <- setMarFilter(gds,
                      id = getMarID(gds)[1:100],
                      missing = 0.2,
                      dp = c(5, Inf))

# Check the number of the retained markers.
nmar(gds)

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

# Check the number of the markers again.
nmar(gds)

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

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