The pcaExplorer package

Main functions and info on the 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