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

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Documentation for package ‘GenomicSuperSignature’ version 1.0.1

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
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