thinMarker: Remove markers potentially having redundant information.

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

Remove markers potentially having redundant information.

Description

Markers within the length of the sequenced reads (usually ~ 150 bp, up to your sequencer) potentially have redundant information and those will cause unexpected errors in error correction which assumes independency of markers each other. This function only retains the first marker or the least missing rate marker from the markers locating within the specified stretch.

Usage

thinMarker(object, range = 150, ...)

## S4 method for signature 'GbsrGenotypeData'
thinMarker(object, range)

Arguments

object	A GbsrGenotypeData object.
range	A integer value to indicate the stretch to search markers.
...	Unused.

Details

This function search valid markers from the first marker of each chromosome and compare its physical position with a neighbor marker. If the distance between those markers are equal or less then range, one of them which has a larger missing rate will be removed (labeled as invalid marker). When the first marker was retained and the second marker was removed as invalid marker, next the distance between the first marker and the third marker will be checked and this cycle is repeated until reaching the end of each chromosome. Run validMar() to check the valid SNP markers.

Value

A GbsrGenotypeData object with 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)

# Summarize genotype count information to be used in thinMarker().
gds <- countGenotype(gds)
gds <- thinMarker(gds, range = 150)

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

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