MissingRate {SeqSQC} | R Documentation |
Function to calculate sample missing rate and to identify sample outlier with high missing rate (> 0.1).
MissingRate(seqfile, remove.samples = NULL)
seqfile |
SeqSQC object, which includes the merged gds file for study cohort and benchmark. |
remove.samples |
a vector of sample names for removal from missing rate check. Could be problematic samples identified from other QC steps, or user-defined samples. |
The value of the outlier column is set to NA for benchmark samples.
a data frame with sample name, sample missing rate, and an indicator of whether the sample has a missing rate greater than 0.1.
Qian Liu qliu7@buffalo.edu
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 <- MissingRate(seqfile, remove.samples=NULL) res.mr <- QCresult(seqfile)$MissingRate tail(res.mr)