Visual and interactive gene expression analysis


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Documentation for package ‘phantasus’ version 1.24.0

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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).