IBDRemove: Obtain the problematic sample list from IBD relatedness.

In Liubuntu/SeqSQC: A bioconductor package for sample quality check with next generation sequencing data

Obtain the problematic sample list from IBD relatedness.

Description

Function to extract the related sample pairs from IBD results, and to generate the sample list for removal from the related pairs based on sample missing rate.

Usage

IBDRemove(seqfile, all = FALSE)

Arguments

seqfile	SeqSQC object, with IBD results.
all	whether to check the IBD for all sample pairs (including the benchmark samples). The default is FALSE.

Value

a list of 2 elements: $ibd.pairs is a data frame with 5 columns including sample names(id1, id2), IBD coefficients of k0 and k1, and kinship for samples with cryptic relatedness. $ibd.remove is a vector of samples to be removed, which are generated by extracting the sample with higher missing rate in each problematic sample pair.

Author(s)

Qian Liu [e-mail]

Examples

load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC"))
gfile <- system.file("extdata", "example.gds", package="SeqSQC")
seqfile <- SeqSQC(gdsfile = gfile, QCresult = QCresult(seqfile))
seqfile <- IBDCheck(seqfile, remove.samples=NULL, LDprune=TRUE, missing.rate=0.1)
IBDRemove(seqfile)

Liubuntu/SeqSQC documentation built on April 12, 2024, 6:39 p.m.