Question submitted by email:
I’m trying to use the regression function in SeqVarTools but I keep getting error about sample id’s not matching when creating SeqVarData, e.g.
# Get the sample ids and force them to match sampleIds <- data.frame( sample.id=seqGetData(gds, 'sample.id') ) phenos <- merge(sampleIds, phenos, sort=F) seqSetFilter(gds, sample.id=phenos$sample.id) phenosDF <- AnnotatedDataFrame(phenos) assocData <- SeqVarData(gds, phenosDF)
It looks like the SeqVarData is ignoring the seqSetFilter command when creating SeqVarData. Is there a way to get around this?