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

to do:

• "IBDRemove.R". if QCresult(seqfile)$MissingRate is missing, recalculate the missing rate by opening the gfile connection. todo: if missing, then run seqfile <- MissingRate(seqfile) and extract the missing rate info. -- done!
• "plotInbreeding", interactive, xlab, ylab, refer to plotSexCheck. -- done.
• "dataset_docum.R". to document all files that are under inst/extdata/... -- done for all 5 files. (except "sampleQCreport.Rmd" and "metadata.csv")
• "PCACheck.R", add an argumnent of "npcs=4" for the # of pc axis to use for pop prediction in SVM. -- done.

SeqSQC documentation built on Nov. 8, 2020, 5:03 p.m.