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

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
 }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(GGBase)
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGBase/MAFfilter.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MAFfilter
> ### Title: Filter genotype contents of an smlSet according to certain SNP
> ###   allele frequency features.
> ### Aliases: MAFfilter GTFfilter dropMonomorphies
> ### Keywords: models
> 
> ### ** Examples
> 
> if (file.exists(system.file("parts/20.rda", package="GGtools"))) {
+  c20 = getSS("GGtools", "20")
+  c20
+  c20f = MAFfilter(c20, lower=.05)
+  c20f
+  }
SnpMatrix-based genotype set:
number of samples:  90 
number of chromosomes present:  1 
annotation: illuminaHumanv1.db 
Expression data dims: 47293 x 90 
Total number of SNP: 55039 
Phenodata: An object of class 'AnnotatedDataFrame'
  sampleNames: NA06985 NA06991 ... NA12892 (90 total)
  varLabels: famid persid ... male (7 total)
  varMetadata: labelDescription
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>