tests/testthat/test_pcasamples.R
In federicomarini/pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach
library(pcaExplorer)
context("Checks on the pca on the samples")
library(DESeq2)
dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
rlt <- rlogTransformation(dds)
pcaobj <- prcomp(t(assay(rlt)))
colData(dds)
pcaplot(rlt)
dat <- pcaplot(rlt, returnData = TRUE)
pcaplot(rlt, intgroup = c("condition", "tissue"))
dat <- pcaplot(rlt, intgroup = c("condition", "tissue"), returnData = TRUE)
expect_error(pcaplot(rlt, intgroup = "foo"))
pcascree(pcaobj)
pcascree(pcaobj, type = "cev")
expect_error(pcascree(pcaobj, type = "foo"))
federicomarini/pcaExplorer documentation built on April 8, 2024, 3:15 a.m.
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library(pcaExplorer)
context("Checks on the pca on the samples")
library(DESeq2)
dds <- makeExampleDESeqDataSet_multifac(betaSD_condition = 3, betaSD_tissue = 1)
rlt <- rlogTransformation(dds)
pcaobj <- prcomp(t(assay(rlt)))
colData(dds)
pcaplot(rlt)
dat <- pcaplot(rlt, returnData = TRUE)
pcaplot(rlt, intgroup = c("condition", "tissue"))
dat <- pcaplot(rlt, intgroup = c("condition", "tissue"), returnData = TRUE)
expect_error(pcaplot(rlt, intgroup = "foo"))
pcascree(pcaobj)
pcascree(pcaobj, type = "cev")
expect_error(pcascree(pcaobj, type = "foo"))
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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