Description Usage Arguments Value Author(s) Examples
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.
1 |
seqfile |
SeqSQC object, with IBD results. |
all |
whether to check the IBD for all sample pairs (including the benchmark samples). The default is FALSE. |
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.
Qian Liu qliu7@buffalo.edu
1 2 3 4 5 | 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)
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