MAFfilter: Filter genotype contents of an smlSet according to certain...
In GGBase: GGBase infrastructure for genetics of gene expression package GGtools

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`	`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

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
 }

GGBase documentation built on Nov. 8, 2020, 5:45 p.m.

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