IBDRemove {SeqSQC} | R Documentation

## 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 qliu7@buffalo.edu

### 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)

[Package SeqSQC version 1.8.1 Index]