Function reference • pcaExplorer

The pcaExplorer package Main functions and info on the `pcaExplorer` package
`pcaExplorer-package` `pcaExplorer-pkg`	pcaExplorer: analyzing time-lapse microscopy imaging, from detection to tracking
`pcaExplorer()`	Explore a dataset from a PCA perspective
Working with Principal Components Functions for working efficiently with Principal Components
`pcaplot()`	Sample PCA plot for transformed data
`pcaplot3d()`	Sample PCA plot for transformed data
`pcascree()`	Scree plot of the PCA on the samples
`correlatePCs()`	Principal components (cor)relation with experimental covariates
`genespca()`	Principal components analysis on the genes
`hi_loadings()`	Extract genes with highest loadings
`plotPCcorrs()`	Plot significance of (cor)relations of covariates VS principal components
Annotation and Functional interpretation Functions for annotating and performing functional interpretation
`get_annotation()`	Get an annotation data frame from biomaRt
`get_annotation_orgdb()`	Get an annotation data frame from org db packages
`topGOtable()`	Extract functional terms enriched in the DE genes, based on topGO
`pca2go()`	Functional interpretation of the principal components
`limmaquickpca2go()`	Functional interpretation of the principal components, based on simple overrepresentation analysis
Expression data exploration
`pair_corr()`	Pairwise scatter and correlation plot of counts
`distro_expr()`	Plot distribution of expression values
`geneprofiler()`	Extract and plot the expression profile of genes
`makeExampleDESeqDataSet_multifac()`	Make a simulated DESeqDataSet for two or more experimental factors

Reference

The pcaExplorer package

Working with Principal Components

Annotation and Functional interpretation

Expression data exploration