MAFfilter {GGBase} | R Documentation |
Filter genotype contents of an smlSet according to certain SNP allele frequency features.
MAFfilter(x, lower = 0, upper = 1) GTFfilter(x, lower = 0) dropMonomorphies(sms)
x |
|
sms |
|
lower |
lower bound on MAF or GTF to allow retention of associated locus |
upper |
upper bound on MAF or GTF to allow retention of associated locus |
uses col.summary
to compute MAF or GTF.
dropMonomorphies
also uses col.summary.
smlSet-class
instance
VJ Carey <stvjc@channing.harvard.edu>
if (file.exists(system.file("parts/20.rda", package="GGtools"))) { c20 = getSS("GGtools", "20") c20 c20f = MAFfilter(c20, lower=.05) c20f }