GGBase (version 3.34.0)

MAFfilter: Filter genotype contents of an smlSet according to certain SNP allele frequency features.

Description

Filter genotype contents of an smlSet according to certain SNP allele frequency features.

Usage

MAFfilter(x, lower = 0, upper = 1)
GTFfilter(x, lower = 0)
dropMonomorphies(sms)

Arguments

x

smlSet-class instance

sms

smlSet-class instance

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

Value

smlSet-class instance

Details

uses col.summary to compute MAF or GTF. dropMonomorphies also uses col.summary.

Examples

if (file.exists(system.file("parts/20.rda", package="GGtools"))) {
 c20 = getSS("GGtools", "20")
 c20
 c20f = MAFfilter(c20, lower=.05)
 c20f
 }