beadarraySNP (version 1.38.0)

calculateLOH: Determine LOH in experiment

Description

Using pairings of normal and tumor samples the LOH pattern is determined

Usage

calculateLOH(object, grouping, NorTum = "NorTum", ...)
calculateLair(object, grouping = NULL, NorTum = "NorTum", min.intensity = NULL,  use.homozygous.avg = FALSE)

Arguments

object

SnpSetIllumina object

grouping

Factor to show which samples belong together (are of the same individual)

NorTum

character vector or factor. Elements containing "N" are considered to be the normal sample

min.intensity

numeric

use.homozygous.avg

logical

...

extra arguments for link{heterozygousSNPs}

Value

For calculateLOH a SnpSetIllumina object with loh and nor.gt matrices in assayData. loh is a logical matrix, and nor.gt is a character matrix containing the genotypes of the corresponding normal sample For calculateLair a SnpSetIllumina object with lair matrix in assayData. lair is the lesser allele intensity ratio. If a corresponding normal sample is found, it is taken as reference. Else the genotypes of normal samples are taken as a reference

Details

The heterozygous SNPs of the normal sample are inspected for changes. SNPs where the genotype of the test sample are homozygous are set to TRUE

See Also

SnpSetIllumina-class