tests/testthat/test_size_factor_iterate.R
In nlhuong/ZeroInflatedDESeq2: Differential gene expression analysis based on the negative binomial distribution
true.sf <- 2^(rep(c(-2,-1,0,0,1,2),each=2))
dds <- makeExampleDESeqDataSet(sizeFactors=true.sf, n=100)
cts <- counts(dds)
idx <- cbind(seq_len(nrow(cts)), sample(ncol(dds), nrow(cts), replace=TRUE))
cts[idx] <- 0L
cts[1,1] <- 1000000L # an outlier
counts(dds) <- cts
dds <- estimateSizeFactors(dds, type="iterate")
sf <- sizeFactors(dds)
coefs <- coef(lm(sf ~ true.sf))
expect_true(abs(coefs[1]) < .1)
expect_true(abs(coefs[2] - 1) < .1)
nlhuong/ZeroInflatedDESeq2 documentation built on May 23, 2019, 9:06 p.m.
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true.sf <- 2^(rep(c(-2,-1,0,0,1,2),each=2))
dds <- makeExampleDESeqDataSet(sizeFactors=true.sf, n=100)
cts <- counts(dds)
idx <- cbind(seq_len(nrow(cts)), sample(ncol(dds), nrow(cts), replace=TRUE))
cts[idx] <- 0L
cts[1,1] <- 1000000L # an outlier
counts(dds) <- cts
dds <- estimateSizeFactors(dds, type="iterate")
sf <- sizeFactors(dds)
coefs <- coef(lm(sf ~ true.sf))
expect_true(abs(coefs[1]) < .1)
expect_true(abs(coefs[2] - 1) < .1)
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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