calculateLOH {beadarraySNP}R Documentation

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}

Details

~~ If necessary, more details than the description above ~~

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

Author(s)

Jan Oosting

See Also

SnpSetIllumina-class


[Package beadarraySNP version 1.6.0 Index]