Visual and interactive gene expression analysis

Documentation for package ‘phantasus’ version 1.0.2

calcPCA	Principal Component Analysis.
checkGPLs	Check possible annotations for GEO Dataset.
checkPreloadedNames	Check names inside preloaded file
createES	Create ExpressionSet.
es	Example dataset
getES	Load ExpressionSet by GEO identifier
getGDS	Load ExpressionSet from GEO Datasets
getGSE	Load ExpressionSet from GEO Series
gseaPlot	Returns path to an svg file with enrichment plot
limmaAnalysis	Differential Expression analysis.
loadGEO	Load GEO Dataset.
loadPreloaded	Load GEO Dataset.
performKmeans	K-means clusterisation.
preloadedDirExists	Check existence of phantasusPreloadedDir
read.gct	Reads ExpressionSet from a GCT file.
reparseCachedESs	Reparse cached expression sets from GEO.
servePhantasus	Serve phantasus.
shinyGAMAnalysis	Constructs data frame with gene annotations and submits it into Shiny GAM web-server
subsetES	Subsets es, if rows or columns are not specified, all are retained
write.gct	Saves ExpressionSet to a GCT file (version 1.3).