Find regions of homozygous SNPs

Description

Analyze affected material without corresponding unaffected material in order to find regions that contain stretches of homozygous SNPs as an indication of loss of heterozygosity (LOH)

Usage

heterozygosity(genotype, decay = 0.8, threshold = 0.1)

Arguments

Details

The method calculates how long the stretch of homozygous SNPs is for each element delay and threshold can be set to skip individual heterozygous probes in a longer stretch of homozygous probes. The default setting tolerate 1 erroneous heterozygous SNP every 10 homozygous SNPs. Set threshold at 1 to stop discarding hetrozygous SNPs

Value

A numeric vector with the same length as genotype is returned. Higher values, of 15 and higher, indicate regions of LOH

Author(s)

Jan Oosting

See Also

compareGenotypes, heterozygousSNPs

Examples

  data(chr17.260)
  plot(heterozygosity(exprs(chr17.260)[,"514TV"]))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(beadarraySNP)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: quantsmooth
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve

Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarraySNP/heterozygosity.Rd_%03d_medium.png", width=480, height=480)
> ### Name: heterozygosity
> ### Title: Find regions of homozygous SNPs
> ### Aliases: heterozygosity
> ### Keywords: manip
> 
> ### ** Examples
> 
>   data(chr17.260)
>   plot(heterozygosity(exprs(chr17.260)[,"514TV"]))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>