Man pages for fchen365/surf
Statistical Utility for RBP (RNA binding protein) Functions
| abs.max | L-infinity norm |
| addGeneTx | Add identifiers of genes and transcripts Fill up missing... |
| aggregateAUCbyCondition | Aggregate AUC by sample condition |
| annotateEvent | Annotate AS events (generate feature bins) |
| calculateAUC | Calculate AUC |
| c_granges | Concatenate a list of GRanges |
| clusterByGroup | Hierarchical clustering of rows by groups |
| countLogicRle | Count number of 'TRUE' from a logical rle |
| daseq | Differential activity analysis (DASeq) |
| daseqResults | DASeq Results |
| daseqResults-class | DASeq class |
| diffAUC | Differential activity (via AUC) |
| drseq | DrSeq |
| drseqCount | Construct DrSeq Data |
| drseqFilter | Screen SURF training samples |
| drseqFit | DrSeq Fit |
| drseqResults | DrSeq Results |
| drseqResults-class | DrSeq class |
| fa.plot | Functional association plot |
| faseq | DASeq |
| faseqCount | Construct FASeq Data Set |
| faseqFit | Functional Association using Sequencing data |
| faseqInfer | Functional association inference |
| faseqResults | FASeq Results |
| faseqResults-class | FASeq class |
| fat | Perform the functional association test (FAT) |
| featureCounts | Customized 'featureCounts' |
| findAdjacentFeature | Find adjacent features of given feature |
| findBodyFeature | Find body features |
| findNeighborFeature | Find features on the (upstream or downstream) constitutive... |
| genePartsList | FASeq results |
| getASName | ATR event name |
| getAUC | Get AUC |
| getControlSet | Get control sets |
| getEES | Get exon end site from exon parts list |
| getESS | Get exon start site from exon parts list |
| getEvent | Enumerate AS events This will not merge SE events across... |
| getFeature | Generate location features |
| getIsoAS | Get AS events for one isoform (decision tree) |
| getIsoPartsList | Parse isoform parts list from annotation |
| getMultiTxGene | Find genes that contain multiple transcripts |
| getRankings | Build gene/transcript rankings for each sample |
| getTargetSet | Get target set based on 'inferredFeature' |
| heatmapAUC | Heatmap of AUC score |
| import | Import annotation files |
| inferredFeature | Extract SURF-inferred location features |
| list_rbind | Bind list by row into data.frame |
| numberAS | Enumerate AS events |
| parseEvent | Parse ATR events from genome annotation |
| plotDispFunc | Plot Dispersion Functions |
| prepDrseqAnno | Prepare DrSeq annotation files |
| sampleData | Sample Data |
| stream | Reconstruct exon parts list to isoform parts list |
| surf-class | SURF class |
| volcano.plot | Volcano plot |
