heterozygousSNPs: Retrieve heterozygous SNPs

Description

Heterozygous SNPs are determined based on quality score criteria

Usage

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

Arguments

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

Value

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

Details

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.

Examples

Run this code

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