MAFfilter {GGBase} | R Documentation

## 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

### Details

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

### Value

`smlSet-class` instance

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

### Examples

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

[Package GGBase version 3.48.0 Index]