heterozygousSNPs: Retrieve heterozygous SNPs
In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description Usage Arguments Details Value Note Author(s) See Also Examples

View source: R/SnpSetIlluminaGenotypes.R

Heterozygous SNPs are determined based on quality score criteria

1 2	heterozygousSNPs(object, threshold=0.9, useQuality=TRUE, relative=TRUE, percentile=FALSE)

`object`	class SnpSetIllumina
`threshold`	numeric (0:1) minimum quality score to be called heterozygous
`useQuality`	logical, use quality score
`relative`	logical, use quality score relative to GTS, see details
`percentile`	logical, use percentage of probes above threshold

This function presumes that the specificity for determining heterozygity is more important than the sensitivity, and will therefore only call probes heterozygous if that can be done with high certainty.
The Illumina genotyping software calculates two quality measures: gen train score (GTS) and gen call score (GCS). The GTS is a measure for how well clusters can be recognized in a training set. This value is probe specific, and the same for all samples in an experiment. The GCS is a probe-specific, sample specific value that measures how close a probe in a sample is to the clusters determined in the training step. This value is always lower than the GTS for a probe.
read.SnpSetIllumina will put GCS into the callProbability element of the assaydata slot and the GTS into the featureData slot. The function uses these locations to retrieve the necessary information.
If relative is FALSE then the raw GCS values are compared to the threshold. In this case a threshold of around 0.5 should be used. If relative is TRUE then GCS/GTS is compared to the threshold and threshold should be around 0.9.
With percentile=TRUE the threshold quantile is calculated for each sample, and only probes with higher scores can be called heterozygous. A threshold of around 0.2 seems to work fine usually.

This function returns a logical matrix with same dimensions as object.

The purpose of the function is to separate heterozygous probes from non-heterozygous probes. In tumor samples the determination of the genotype can be difficult, because of aneuploidy and the fact that a sample is often a mixture of normal and tumor cells.

Jan Oosting

SnpSetIllumina-class

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  data(chr17.260)
  plot(heterozygosity(heterozygousSNPs(chr17.260[,"514TV"])),col="red",pch="x")
  points(heterozygosity(exprs(chr17.260)[,"514TV"]))