Description Usage Arguments Details Value Author(s) Examples
Function to calculate the X chromosome inbreeding coefficient and to predict sample gender.
1 2 |
seqfile |
SeqSQC object, which includes the merged gds file for study cohort and benchmark. |
remove.samples |
a vector of sample names for removal from sex check. Could be problematic samples identified from previous QC steps, or user-defined samples. |
missing.rate |
to use the SNPs with "<= |
ss.cutoff |
the minimum sample size (300 by default) to apply the MAF filter. This sample size is the sum of study samples and the benchmark samples of the same population as the study cohort. |
maf |
to use the SNPs with ">= |
... |
Arguments to be passed to other methods. |
Samples are predicted to be female or male if the
inbreeding coefficient is below 0.2, or greater than 0.8,
respectively. The samples with discordant reported gender and
predicted gender are considered as problematic. When the
inbreeding coefficient is within the range of [0.2, 0.8], <e2><80><9c>0<e2><80><9d>
is shown in the column of pred.sex
to indicate ambiguous
gender, which is not considered as problematic.
a data frame with sample name, reported gender, x chromosome inbreeding coefficient, and predicted gender.
Qian Liu qliu7@buffalo.edu
1 2 3 4 5 6 | 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 <- SexCheck(seqfile, remove.samples=NULL, missing.rate=0.1)
res.sexc <- QCresult(seqfile)$SexCheck
tail(res.sexc)
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