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mikelove/fastVST.R

Created August 28, 2015 17:14
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fast VST
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fastVST.R
library(DESeq2)
# simulate data
dds <- makeExampleDESeqDataSet(n=80000,m=100)
# this takes 10 seconds on my machine
dds <- estimateSizeFactors(dds)
baseMean <- rowMeans(counts(dds, normalized=TRUE))
sum(baseMean > 1)
idx <- sample(which(baseMean > 5), 1000)
dds.sub <- dds[idx, ]
dds.sub <- estimateDispersions(dds.sub)
dispersionFunction(dds) <- dispersionFunction(dds.sub)
vsd <- varianceStabilizingTransformation(dds, blind=FALSE)
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