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

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Documentation for package ‘InPAS’ version 2.14.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

$-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