Man pages for haibol2016/InPAS
Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data
| addChr2Exclude | Add a globally-applied requirement for filtering out... |
| addInPASEnsDb | Add a globally defined EnsDb to some InPAS functions. |
| addInPASGenome | Add a globally defined genome to all InPAS functions. |
| addInPASOutputDirectory | Add a globally defined output directory to some InPAS... |
| addInPASTxDb | Add a globally defined TxDb for InPAS functions. |
| addLockName | Add a filename for locking a SQLite database |
| adjust_distalCPs | Adjust distal CP sites by the cleanUpdTSeq algorithm |
| adjust_proximalCPs | Adjust the proximal CP sites |
| adjust_proximalCPsByNBC | adjust the proximal CP sites by using Naive Bayes classifier... |
| adjust_proximalCPsByPWM | adjust the proximal CP sites by matching PWM |
| assemble_allCov | Assemble coverage files for a given chromosome for all... |
| assign_feature | Helper function to label the last component of a genomic... |
| calculate_mse | Calculate mean squared errors (MSE) |
| compensation | Compensate the coverage with GC-content or mappability |
| dot-onAttach | A function called upon a package is attached to the search... |
| extract_UTR3Anno | extract 3' UTR information from a GenomicFeatures::TxDb... |
| fft.smooth | Smoothing using Fast Discrete Fourier Transform |
| filter_testOut | filter 3' UTR usage test results |
| find_minMSEDistr | Visualization of MSE profiles, 3' UTR coverage and minimal... |
| find_valleyBySpline | Find major valleys after spline smoothing |
| gcComp | Calculate weights for GC composition |
| gcContents | helper function to calculate chromosome/scaffold level GC... |
| getChr2Exclude | Get a globally-applied requirement for filtering scaffolds. |
| get_chromosomes | Identify chromosomes/scaffolds for CP site discovery |
| get_depthWeight | Calculate the depth weight for each sample or each... |
| getInPASEnsDb | Get the globally defined EnsDb. |
| getInPASGenome | Get the globally defined genome |
| getInPASOutputDirectory | Get the path to a output directory for InPAS analysis |
| getInPASSQLiteDb | Get the path to an SQLite database |
| getInPASTxDb | Get the globally defined TxDb. |
| get_lastCDSUTR3 | Extract the last unspliced region of each transcript |
| getLockName | Get the path to a file for locking the SQLite database |
| get_PAscore | Calculate the CP score |
| get_PAscore2 | calculate the CP score |
| get_regionCov | Get coverage for 3' UTR and last CDS regions on a single... |
| get_seqLen | Get sequence lengths for chromosomes/scaffolds |
| get_ssRleCov | Get Rle coverage from a bedgraph file for a sample |
| get_totalCov | Calculate the total coverage |
| get_usage4plot | prepare coverage data and fitting data for plot |
| get_UTR3CDS | Get 3' UTRs and their last CDS regions based on CP sites |
| get_UTR3eSet | prepare 3' UTR coverage data for usage test |
| get_UTR3region | extract long and short 3UTR region |
| get_UTR3TotalCov | extract coverage of 3' UTR for CP sites prediction |
| get_zScoreCutoff | Calculate local background cutoff value |
| InPAS | A package for identifying novel Alternative PolyAdenylation... |
| mapComp | Calculate weights for mappability-base coverage correction |
| parse_TxDb | Extract gene models from a TxDb object |
| plot_utr3Usage | Visualize the dPDUI events using ggplot2 |
| polish_CPs | polish the searching results of CP sites |
| remove_convergentUTR3s | remove the converging candidates 3' UTRs LIKE UTR3___UTR3 |
| run_coverageQC | Quality control on read coverage over gene bodies and 3UTRs |
| run_fisherExactTest | Run Fisher Exact Test for differential usage of 3' UTRs for a... |
| run_limmaAnalysis | use limma to analyze the PDUI |
| run_singleGroupAnalysis | do analysis for single group samples |
| run_singleSampleAnalysis | do APA analysis for a single sample |
| search_CPs | Estimate the CP sites for UTRs on a given chromosome |
| search_distalCPs | search distal CP sites |
| search_proximalCPs | search proximal CPsites |
| set_globals | Set up global variables for an InPAS analysis |
| setup_CPsSearch | prepare data for predicting cleavage and polyadenylation (CP)... |
| setup_GSEA | prepare files for GSEA analysis |
| setup_parCPsSearch | Prepare data for predicting cleavage and polyadenylation (CP)... |
| setup_sqlitedb | Create an SQLite database for storing metadata and paths to... |
| test_dPDUI | do test for dPDUI |
| trim_seqnames | Filter sequence names from a BSgenome object |
| UTR3eSet-class | UTR3eSet-class and its methods |
| utr3.mm10 | Annotation of 3' UTRs for mouse (mm10) |
