Man pages for shbrief/PCAGenomicSignatures
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
| 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 |
| dot-calculateSilhouetteWidth | Calculate Silhouette Information of RAVs |
| dot-loadingCor | Validating new dataset |
| dot-RAVName | Formatting RAV name |
| 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 |
| 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 |
| heatmapTable | Validation result in heatmap format |
| meshTable | Build a two-column word/frequency table |
| miniAllZ | Subset of allZ matrix constructed from 8 CRC training... |
| 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 |
| 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 |
| res_hcut | Subset of allZ matrix constructed from 8 CRC training... |
| rmNaInf | Remove rows with missing and Inf values from a matrix |
| sampleScoreHeatmap | Plot heatmap of the sample scores |
| subsetEnrichedPathways | Subset enriched pathways of RAV |
| validate | Validate new datasets |
| validatedSignatures | Validation result in data frame |
