Man pages for yue-wang-biomath/RgnTX
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
| adjustMultipleTesting | Calculate adjusted pvalues |
| calculateShift | Calculate positional shifting over transcriptome |
| distanceTx | Evaluation function |
| extractRegions | Extract regions |
| getFormatCorrect | getFormatCorrect |
| getPermSpaceByFeatures | Get permutation space for features |
| getPermSpaceByTxID | Get permutation space by specifying transcript ids |
| getPermSpaceByType | Get permutation space by specifying type |
| getPvalZscore | getPvalZscore |
| getStopCodon | getStopCodon |
| getTransInfo | Get transcript information |
| GRanges2GRangesList | Convert a GRanges object to a GRangesList object |
| GRangesList2GRanges | Convert a GRangesList object to a GRanges object |
| overlapCountsTx | Evaluation function |
| overlapCountsTxIA | Evaluation function |
| overlapWidthTx | Evaluation function |
| permTestTx | Perform permutation test |
| permTestTx_customAll | Perform permutation test |
| permTestTx_customPick | Perform permutation test |
| permTestTxIA | Perform permutation test |
| permTestTxIA_customPick | Perform permutation test |
| plotPermResults | Plot permutation test results |
| plotShiftedZScoreTx | Plot shifted z scores |
| randomizeFeaturesTx | Randomize features into transcriptome |
| randomizeFeaturesTxIA | Randomize features into transcriptome |
| randomizeTransByOrder | Randomize features into transcriptome |
| randomizeTx | Get randmized regions over transcriptome |
| shiftedZScoreTx | Calculate shifted z scores over transcripts |
| shiftExonTx | Shift regions over transcripts |
| shiftTx | Shift over transcripts |
| vector2GRangesList | vector2GRangesList |
