genotype filter methods

Description

useful genotype filters

Usage

hetFilt(x, ...)

## S4 method for signature 'ASEset'
hetFilt(x, source = "genotype", ...)

Arguments

Details

hetFilt returns TRUE if the samples is heterozygote, based on stored genotype information present in the phase data.

Author(s)

Jesper R. Gadin, Lasse Folkersen

Examples

#load example data
data(ASEset)
a <- ASEset

genotype(a) <- inferGenotypes(a)
hets <- hetFilt(a) 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(AllelicImbalance)
Loading required package: grid
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: GenomicAlignments
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AllelicImbalance/ASEset-filters.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ASEset-filters
> ### Title: genotype filter methods
> ### Aliases: ASEset-filters hetFilt hetFilt,ASEset-method
> ### Keywords: filter
> 
> ### ** Examples
> 
> 
> #load example data
> data(ASEset)
> a <- ASEset
> 
> genotype(a) <- inferGenotypes(a)
> hets <- hetFilt(a) 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>