heterozygosity: Find regions of homozygous SNPs

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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"]))

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.