Visual and interactive gene expression analysis

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Documentation for package ‘phantasus’ version 1.24.0

• 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
createDockerConf	Creates default docker conf file Function creates default docker user configuration file based on provided 'setup_file' or on default parameters if 'setup_file' doesn't exist. If 'user_conf_file' exists function does nothing.
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
getPhantasusConf	Read Phantasus Config
gseaPlot	Returns path to an svg file with enrichment plot
limmaAnalysis	Differential Expression analysis.
loadCounts	Loads expression data from .h5 count files. Only samples with counted expression are kept. If es already containts expression data it is returned as is.
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.
setupPhantasus	Setup phantasus. Read user config file ( or create default one) and fill 'cache_root' using sources in 'file'.
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
updateARCHS4	Update archs4 files.
updateARCHS4meta	Update ARCHS4 meta files
updateCountsMeta	Update meta-data for counts collections
updateDEE2meta	Update DEE2 meta files
write.gct	Saves ExpressionSet to a GCT file (version 1.3).