# Visual and interactive gene expression analysis

## Documentation for package ‘phantasus’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

adjustDataset | Adjust dataset
annotationDBMeta | Create meta file for AnnotationDB
calcPCA | Principal Component Analysis.
calculatedAnnotation | Create calculated annotation
checkGPLsFallback | Check possible annotations for GEO Dataset.
collapseDataset | Collapse dataset
colMeansByGroups | Calculate column averages in row groups
convertByAnnotationDB | Map indexes using Annotation DB
createES | Create ExpressionSet.
es | Example dataset
fgseaExample | Example pathway data.frame for fgsea tool
generatePreloadedSession | Generate files for preloaded session from a session link.
getArchs4Files | Returns list of ARCHS4 hdf5 files with expression data
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.
loadFromARCHS4 | Loads expression data from ARCHS4 count files. Only sapmles with counted expression are kept. If es already containts expression data it is returned as is.
loadGEO | Load GEO Dataset.
loadPreloaded | Load GEO Dataset.
performKmeans | K-means clusterisation.
queryAnnotationDBMeta | Get meta list for annotationDB files
read.gct | Reads ExpressionSet from a GCT file.
reparseCachedESs | Reparse cached expression sets from GEO.
reproduceInR | Reproduce session in R code
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).