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

## Documentation for package ‘GenomicSuperSignature’ version 1.2.0

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

## Help Pages

.calculateSilhouetteWidth | Calculate Silhouette Information of RAVs
.loadingCor | Validating new dataset
.PCAGenomicSignatures | PCAGenomicSignatures-class
.RAVName | Formatting RAV name
annotatePC | Annotate top PCs from the dataset
annotateRAV | Search the top enriched pathways for RAV
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
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
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
makeGeneList | Order genes in loading vectors
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
msigdb_gsea | MSigDB GSEA results
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-dimentional 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
rowNorm | z-score each row of the data
run_gsea | GSEA on pre-ordered gene lists
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
subsetGSEA | Subset GSEA output
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