Man pages for shbrief/GenomicSuperSignature
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

annotatePCAnnotate top PCs from the dataset
annotateRAVSearch the top enriched pathways for RAV
availableRAVmodelList the available RAVmodels
buildAvgLoadingCalculate average loadings of each cluster
calculateScoreCalculate the validation score for a new dataset
dot-calculateSilhouetteWidthCalculate Silhouette Information of RAVs
dot-loadingCorValidating new dataset
dot-RAVNameFormatting RAV name
drawWordcloudDraw wordcloud using the collection of RAVs' MeSH terms
droplistMeSH terms to be excluded in drawWordcloud function
extractPCPCA on gene expression profile
filterListRAVs that will output with quality-control messages
findKeywordInRAVFind the rank of your keyword in the RAV's GSEA annotation
findSignatureFind the RAVs with the keyword-containing enriched pathways
findStudiesInClusterFind the studies contributing each RAV
GenomicSignatures-classVirtual class inherited from SummarizedExperiment
GenomicSignatures-methodsMethods and accesors for 'GenomicSignatures' object
getModelDownload a PCAGenomicSignatures model
getRAVInfoExtract information on a specific RAV
getStudyInfoExtract information on a specific training dataset
heatmapTableValidation result in heatmap format
meshTableBuild a two-column word/frequency table
miniAllZSubset of allZ matrix constructed from 8 CRC training...
miniRAVmodelRAVmodel from 536 studies, annotated with MSigDB C2
miniTCGASubset of TCGA-COAD and TCGA-BRCA RNA sequencing datasets
PCAGenomicSignaturesConstruct 'PCAGenomicSignatures' object
PCAGenomicSignatures-classPCAGenomicSignatures-class
PCAGenomicSignatures-methodsMethods and accesors for 'PCAGenomicSignatures' object
PCinRAVExtract the list of PCs in a cluster
plotAnnotatedPCATwo-dimensional PCA plot with the PC annotation
plotValidatePlot validation results in an interactive graph
res_hcutSubset of allZ matrix constructed from 8 CRC training...
rmNaInfRemove rows with missing and Inf values from a matrix
sampleScoreHeatmapPlot heatmap of the sample scores
subsetEnrichedPathwaysSubset enriched pathways of RAV
validateValidate new datasets
validatedSignaturesValidation result in data frame
shbrief/GenomicSuperSignature documentation built on May 3, 2023, 10:07 p.m.