For example, preProcessVCF has functionalImpactScoreCDS but when I open the help document using preProcessVCF I see the second parameter is completely different: outputDir Other parameters also don't match up to those shown in Usage. The documentation could also be more informative. For example, all that the Description section states is
Parse Funseq2 VCF file
Perhaps you could use
\references{
FunSeq2: A Framework for Prioritizing Noncoding Regulatory Variants in Cancer, Yao Fu, Zhu Liu, etc.
}
For example,
preProcessVCFhas functionalImpactScoreCDS but when I open the help document usingpreProcessVCFI see the second parameter is completely different:outputDirOther parameters also don't match up to those shown in Usage. The documentation could also be more informative. For example, all that the Description section states isPerhaps you could use
in the R Documentation file.