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tests/testthat/test_correlatePCs.R
In pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach
library(pcaExplorer)
context("Check that correlations are computed and plotted")
library(DESeq2)
dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
rlt <- rlogTransformation(dds)
pcaobj <- prcomp(t(assay(rlt)))
res <- correlatePCs(pcaobj, colData(dds))
expect_equal(dim(res), c(4, 2))
expect_equal(colnames(res), colnames(colData(dds)))
plotPCcorrs(res)
plotPCcorrs(res, logp = FALSE, pc = 2)
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pcaExplorer documentation built on Nov. 8, 2020, 5:29 p.m.
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library(pcaExplorer)
context("Check that correlations are computed and plotted")
library(DESeq2)
dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
rlt <- rlogTransformation(dds)
pcaobj <- prcomp(t(assay(rlt)))
res <- correlatePCs(pcaobj, colData(dds))
expect_equal(dim(res), c(4, 2))
expect_equal(colnames(res), colnames(colData(dds)))
plotPCcorrs(res)
plotPCcorrs(res, logp = FALSE, pc = 2)
Try the pcaExplorer package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
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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