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| InPAS-package | alternative polyadenylation and cleavage estimations |
| $-method | Class 'UTR3eSet' |
| $<--method | Class 'UTR3eSet' |
| coverageFromBedGraph | read coverage from bedGraph files |
| coverageRate | coverage rate of genes and 3UTRs |
| covThreshold | calculate the cutoff threshold of coverage |
| CPsites | predict the cleavage and polyadenylation(CP) site |
| CPsite_estimation | estimate the cpsites |
| depthWeight | calculate the depth weight for each example |
| distalAdj | adjust distal CP sites by cleanUpdTSeq |
| filterRes | filter results |
| fisher.exact.test | do fisher exact test for two group datasets |
| get.regions.coverage | claculate coverage for giving region |
| getCov | extract coverage from bedgraph file |
| getUTR3eSet | prepare dataset for test |
| getUTR3region | extract long and short 3UTR region |
| InPAS | alternative polyadenylation and cleavage estimations |
| inPAS | do estimation of alternative polyadenylation and cleavage site in one step |
| lastCDSusage | extract coverage of last CDS exon region |
| limmaAnalyze | use limma to analyze the PDUI |
| optimalSegmentation | calculate SSE |
| PAscore | calculate the CP score |
| PAscore2 | calculate the CP score |
| polishCPs | polish the searching results of CP sites |
| prepare4GSEA | prepare the files for GSEA analysis |
| proximalAdj | adjust the proximal CP sites |
| proximalAdjByCleanUpdTSeq | adjust the proximal CP sites by cleanUpdTseq |
| proximalAdjByPWM | adjust the proximal CP sites by PWM |
| removeUTR3__UTR3 | remove the candicates LIKE UTR3___UTR3 |
| searchDistalCPs | search distal CP sites |
| searchProximalCPs | search proximal CPsites |
| seqLen | get sequence lengths |
| singleGroupAnalyze | do analysis for single group samples |
| singleSampleAnalyze | do analysis for single sample |
| sortGR | sort GRanges |
| testUsage | do test for dPDUI |
| totalCoverage | total coverage |
| trimSeqnames | trim the sequence names |
| usage4plot | prepare coverage data and fitting data for plot |
| utr3.danRer10 | 3'UTR annotation for danRer10 obtained from utr3Annotation |
| utr3.hg19 | 3'UTR annotation for hg19 obtained from utr3Annotation |
| utr3.mm10 | 3'UTR annotation for mm10 obtained from utr3Annotation |
| utr3Annotation | extract 3'UTR from TxDb object |
| UTR3eSet | Class 'UTR3eSet' |
| UTR3eSet-class | Class 'UTR3eSet' |
| UTR3TotalCoverage | extract coverage of 3UTR for CP sites prediction |
| UTR3usage | calculate the usage of long and short form of UTR3 |
| utr3UsageEstimation | estimation of 3'UTR usage for each region |
| valley | get the local minimal square standard error (SSE) |
| zScoreThrethold | calculate local background cutoff value |