Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

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Documentation for package ‘GenomicSuperSignature’ version 1.16.1

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

Help Pages

.PCAGenomicSignatures	PCAGenomicSignatures-class
annotatePC	Annotate top PCs from the dataset
annotateRAV	Search the top enriched pathways for RAV
availableRAVmodel	List the available RAVmodels
buildAvgLoading	Calculate average loadings of each cluster
calculateScore	Calculate the validation score for a new dataset
colData	Methods and accesors for 'GenomicSignatures' object
drawWordcloud	Draw wordcloud using the collection of RAVs' MeSH terms
droplist	MeSH terms to be excluded in drawWordcloud function
extractPC	PCA on gene expression profile
filterList	RAVs that will output with quality-control messages
findKeywordInRAV	Find the rank of your keyword in the RAV's GSEA annotation
findSignature	Find the RAVs with the keyword-containing enriched pathways
findStudiesInCluster	Find the studies contributing each RAV
geneSets	Methods and accesors for 'GenomicSignatures' object
geneSets-method	Methods and accesors for 'GenomicSignatures' object
geneSets<-	Methods and accesors for 'GenomicSignatures' object
geneSets<--method	Methods and accesors for 'GenomicSignatures' object
GenomicSignatures-class	Virtual class inherited from SummarizedExperiment
GenomicSignatures-methods	Methods and accesors for 'GenomicSignatures' object
getModel	Download a PCAGenomicSignatures model
getRAVInfo	Extract information on a specific RAV
getStudyInfo	Extract information on a specific training dataset
gsea	Methods and accesors for 'PCAGenomicSignatures' object
gsea-method	Methods and accesors for 'PCAGenomicSignatures' object
gsea<-	Methods and accesors for 'PCAGenomicSignatures' object
gsea<--method	Methods and accesors for 'PCAGenomicSignatures' object
heatmapTable	Validation result in heatmap format
mesh	Methods and accesors for 'PCAGenomicSignatures' object
mesh-method	Methods and accesors for 'PCAGenomicSignatures' object
mesh<-	Methods and accesors for 'PCAGenomicSignatures' object
mesh<--method	Methods and accesors for 'PCAGenomicSignatures' object
meshTable	Build a two-column word/frequency table
metadata	Methods and accesors for 'GenomicSignatures' object
miniAllZ	Subset of allZ matrix constructed from 8 CRC training datasets
miniRAVmodel	RAVmodel from 536 studies, annotated with MSigDB C2
miniTCGA	Subset of TCGA-COAD and TCGA-BRCA RNA sequencing datasets
PCAGenomicSignatures	Construct 'PCAGenomicSignatures' object
PCAGenomicSignatures-class	PCAGenomicSignatures-class
PCAGenomicSignatures-methods	Methods and accesors for 'PCAGenomicSignatures' object
PCAsummary	Methods and accesors for 'PCAGenomicSignatures' object
PCAsummary-method	Methods and accesors for 'PCAGenomicSignatures' object
PCAsummary<-	Methods and accesors for 'PCAGenomicSignatures' object
PCAsummary<--method	Methods and accesors for 'PCAGenomicSignatures' object
PCinRAV	Extract the list of PCs in a cluster
plotAnnotatedPCA	Two-dimensional PCA plot with the PC annotation
plotValidate	Plot validation results in an interactive graph
RAVindex	Methods and accesors for 'GenomicSignatures' object
RAVindex-method	Methods and accesors for 'GenomicSignatures' object
res_hcut	Subset of allZ matrix constructed from 8 CRC training datasets
rmNaInf	Remove rows with missing and Inf values from a matrix
sampleScoreHeatmap	Plot heatmap of the sample scores
show-method	Methods and accesors for 'PCAGenomicSignatures' object
silhouetteWidth	Methods and accesors for 'PCAGenomicSignatures' object
silhouetteWidth-method	Methods and accesors for 'PCAGenomicSignatures' object
silhouetteWidth<-	Methods and accesors for 'PCAGenomicSignatures' object
silhouetteWidth<--method	Methods and accesors for 'PCAGenomicSignatures' object
studies	Methods and accesors for 'PCAGenomicSignatures' object
studies-method	Methods and accesors for 'PCAGenomicSignatures' object
studies<-	Methods and accesors for 'PCAGenomicSignatures' object
studies<--method	Methods and accesors for 'PCAGenomicSignatures' object
subsetEnrichedPathways	Subset enriched pathways of RAV
trainingData	Methods and accesors for 'PCAGenomicSignatures' object
trainingData-method	Methods and accesors for 'PCAGenomicSignatures' object
trainingData<-	Methods and accesors for 'PCAGenomicSignatures' object
trainingData<--method	Methods and accesors for 'PCAGenomicSignatures' object
updateNote	Methods and accesors for 'GenomicSignatures' object
updateNote-method	Methods and accesors for 'GenomicSignatures' object
updateNote<-	Methods and accesors for 'GenomicSignatures' object
updateNote<--method	Methods and accesors for 'GenomicSignatures' object
validate	Validate new datasets
validatedSignatures	Validation result in data frame
version-method	Methods and accesors for 'GenomicSignatures' object