# Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

## Documentation for package ‘InPAS’ version 2.19.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

-package | A package for identifying novel Alternative PolyAdenylation Sites (PAS) based on RNA-seq data
$-method | UTR3eSet-class and its methods
$<--method | UTR3eSet-class and its methods
addChr2Exclude | Add a globally-applied requirement for filtering out scaffolds from all analysis
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 functions.
addInPASTxDb | Add a globally defined TxDb for InPAS functions.
addLockName | Add a filename for locking a SQLite database
assemble_allCov | Assemble coverage files for a given chromosome for all samples
coerce-method | UTR3eSet-class and its methods
extract_UTR3Anno | extract 3' UTR information from a GenomicFeatures::TxDb object
filter_testOut | filter 3' UTR usage test results
find_minMSEDistr | Visualization of MSE profiles, 3' UTR coverage and minimal MSE distribution
getChr2Exclude | Get a globally-applied requirement for filtering scaffolds.
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.
getLockName | Get the path to a file for locking the SQLite database
get_chromosomes | Identify chromosomes/scaffolds for CP site discovery
get_lastCDSUTR3 | Extract the last unspliced region of each transcript
get_regionCov | Get coverage for 3' UTR and last CDS regions on a single chromosome
get_ssRleCov | Get Rle coverage from a bedgraph file for a sample
get_usage4plot | prepare coverage data and fitting data for plot
get_UTR3eSet | prepare 3' UTR coverage data for usage test
InPAS | A package for identifying novel Alternative PolyAdenylation Sites (PAS) based on RNA-seq data
parse_TxDb | Extract gene models from a TxDb object
plot_utr3Usage | Visualize the dPDUI events using ggplot2
run_coverageQC | Quality control on read coverage over gene bodies and 3UTRs
search_CPs | Estimate the CP sites for UTRs on a given chromosome
setup_CPsSearch | prepare data for predicting cleavage and polyadenylation (CP) sites
setup_GSEA | prepare files for GSEA analysis
setup_parCPsSearch | Prepare data for predicting cleavage and polyadenylation (CP) sites using parallel computing
setup_sqlitedb | Create an SQLite database for storing metadata and paths to coverage files
set_globals | Set up global variables for an InPAS analysis
show-method | UTR3eSet-class and its methods
test_dPDUI | do test for dPDUI
utr3.mm10 | Annotation of 3' UTRs for mouse (mm10)
UTR3eSet-class | UTR3eSet-class and its methods