heterozygosity {beadarraySNP} | R Documentation

## 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

`genotype` | character or logical vector, genotypes of affected tissue
`decay` | numeric in range (0,1)
`threshold` | numeric in range (0,1)

### 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"]))

[Package beadarraySNP version 1.53.0 Index]