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heterozygousSNPs(object, threshold=0.9, useQuality=TRUE, relative=TRUE, percentile=FALSE)
logical matrix
with same dimensions as object
.
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.
SnpSetIllumina-class
data(chr17.260)
plot(heterozygosity(heterozygousSNPs(chr17.260[,"514TV"])),col="red",pch="x")
points(heterozygosity(exprs(chr17.260)[,"514TV"]))
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