heterozygosity {beadarraySNP} | R Documentation |
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)
heterozygosity(genotype, decay = 0.8, threshold = 0.1)
genotype |
character or logical vector, genotypes of affected tissue |
decay |
numeric in range (0,1) |
threshold |
numeric in range (0,1) |
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
A numeric vector with the same length as genotype is returned. Higher values, of 15 and higher, indicate regions of LOH
Jan Oosting
compareGenotypes
, heterozygousSNPs
data(chr17.260) plot(heterozygosity(exprs(chr17.260)[,"514TV"]))