compareGenotypes: Compare genotypes

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description

Pairwise comparison of genotypes between unaffected and affected tissue from the same subject

Usage

compareGenotypes(genotypeT, genotypeN)

Arguments

genotypeT	character or logical vector, genotypes of affected tissue
genotypeN	character or logical vector with same length as genotypeT, genotypes of unaffected, normal tissue

Details

Heterozygous probes have one the following values. TRUE, 'H' or 'AB'. All other values are considered homozygous. The primary purpose of the method is to find probes with loss of heterozygosity (LOH), where the unaffected probe is heterozygous and the affected is called homozygous.

Value

A vector with the same length as the arguments where each element can have one of four values

'u'	Uninformative: both affected and normal are homozygous
'i'	Informative: both affected and unaffected heterozygous
'l'	Loss: unaffected heterozygous, affected homozygous
'a'	Artefact: unaffected homozygous, affected heterozygous

Author(s)

Jan Oosting

See Also

heterozygousSNPs

Examples

data(chr17.260)
compareGenotypes(exprs(chr17.260)[,"514TV"],exprs(chr17.260)[,"514NP"])

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