roar: Identify differential APA usage from RNA-seq alignments
Version 1.12.0

Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.

AuthorElena Grassi
Bioconductor views HighThroughputSequencing RNAseq Sequencing Transcription
Date of publicationNone
MaintainerElena Grassi <grassi.e@gmail.com>
LicenseGPL-3
Version1.12.0
URL https://github.com/vodkatad/roar/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("roar")

Getting started

Package overview

Popular man pages

getFisher-method: Private/inner/helper method to perform Fisher test
meanAcrossAssays-method: Private/inner/helper method to get average counts across...
RoarDataset-constructor: Creates a 'RoarDataset' object
RoarDatasetFromFiles-constructor: Creates a 'RoarDataset' object
RoarDatasetMultipleAPAFromFiles-constructor: Creates a 'RoarDatasetMultipleAPA' object
roar-package: Identify differential APA usage from RNA-seq alignments
totalResults-method: Returns a dataframe with results of the analysis for a...
See all...

All man pages Function index File listing

Man pages

checkStep-method: Private/inner/helper method to check the order of the invoked...
combineFisherMethod-method: Private/inner/helper method to combine pvalues of independent...
computePairedPvals-method: Computes pvalues (Fisher test) on the read counts in this...
computePvals-method: Computes pvalues (Fisher test) on the read counts in this...
computeRoars-method: Computes m/M and roar values
cores-method: Method to check how many cores are used by a roar analysis -...
countPrePost-method: Counts reads falling over PRE/POST portions of the given...
countResults-method: Returns a dataframe with results of the analysis for a...
fpkmResults-method: Returns a dataframe with results of the analysis for a...
getFisher-method: Private/inner/helper method to perform Fisher test
meanAcrossAssays-method: Private/inner/helper method to get average counts across...
pvalueCorrectFilter-method: Returns a dataframe with results of the analysis for a...
pvalueFilter-method: Returns a dataframe with results of the analysis for a...
RoarDataset-class: Class '"RoarDataset"'
RoarDataset-constructor: Creates a 'RoarDataset' object
RoarDatasetFromFiles-constructor: Creates a 'RoarDataset' object
RoarDatasetMultipleAPA-class: Class '"RoarDatasetMultipleAPA"'
RoarDatasetMultipleAPA-constructor: Creates a 'RoarDatasetMultipleAPA' object
RoarDatasetMultipleAPAFromFiles-constructor: Creates a 'RoarDatasetMultipleAPA' object
roar-package: Identify differential APA usage from RNA-seq alignments
standardFilter-method: Returns a dataframe with results of the analysis for a...
totalResults-method: Returns a dataframe with results of the analysis for a...

Functions

RoarDataset Man page Source code
RoarDataset-class Man page
RoarDatasetFromFiles Man page Source code
RoarDatasetMultipleAPA Man page Source code
RoarDatasetMultipleAPA-class Man page
RoarDatasetMultipleAPAFromFiles Man page Source code
checkStep Man page Source code
combineFisherMethod Man page Source code
computePairedPvals Man page
computePairedPvals, RoarDataset Man page
computePairedPvals, RoarDatasetMultipleAPA Man page
computePairedPvals,RoarDataset,numeric,numeric-method Man page
computePairedPvals,RoarDatasetMultipleAPA,numeric,numeric-method Man page
computePvals Man page
computePvals, RoarDataset Man page
computePvals, RoarDatasetMultipleAPA Man page
computePvals,RoarDataset-method Man page
computePvals,RoarDatasetMultipleAPA-method Man page
computeRoars Man page
computeRoars, RoarDataset, numeric, numeric Man page
computeRoars, RoarDatasetMultipleAPA, numeric, numeric Man page
computeRoars,RoarDataset-method Man page
computeRoars,RoarDatasetMultipleAPA-method Man page
cores Man page
cores,RoarDataset-method Man page
cores,RoarDatasetMultipleAPA-method Man page
countPrePost Man page
countPrePost,RoarDataset,logical Man page
countPrePost,RoarDataset,logical-method Man page
countPrePost,RoarDataset-method Man page
countPrePost,RoarDatasetMultipleAPA Man page
countPrePost,RoarDatasetMultipleAPA,logical-method Man page
countPrePost,RoarDatasetMultipleAPA-method Man page
countResults Man page
countResults, RoarDataset Man page
countResults, RoarDatasetMultipleAPA Man page
countResults,RoarDataset-method Man page
countResults,RoarDatasetMultipleAPA-method Man page
createRoarMultipleBam Source code
createRoarSingleBam Source code
fpkmResults Man page
fpkmResults, RoarDataset Man page
fpkmResults, RoarDatasetMultipleAPA Man page
fpkmResults,RoarDataset-method Man page
fpkmResults,RoarDatasetMultipleAPA-method Man page
getApaGenesFractions Source code
getApaGenesFractionsMinusStrand Source code
getApaGenesFractionsPlusStrand Source code
getFisher Man page Source code
getPreCoordsSE Source code
meanAcrossAssays Man page Source code
obtainPrePost Source code
pvalueCorrectFilter Man page
pvalueCorrectFilter, RoarDataset Man page
pvalueCorrectFilter, RoarDatasetMultipleAPA Man page
pvalueCorrectFilter,RoarDataset,numeric,numeric,character-method Man page
pvalueCorrectFilter,RoarDatasetMultipleAPA,numeric,numeric,chara Man page
pvalueFilter Man page
pvalueFilter, RoarDataset Man page
pvalueFilter, RoarDatasetMultipleAPA Man page
pvalueFilter,RoarDataset,numeric,numeric-method Man page
pvalueFilter,RoarDatasetMultipleAPA,numeric,numeric-method Man page
roar Man page
roar-package Man page
standardFilter Man page Source code
standardFilter, RoarDataset Man page
standardFilter, RoarDatasetMultipleAPA Man page
standardFilter,RoarDataset,numeric-method Man page
standardFilter,RoarDatasetMultipleAPA,numeric-method Man page
sumFragmentCounts Source code
totalResults Man page
totalResults, RoarDataset Man page
totalResults, RoarDatasetMultipleAPA Man page
totalResults,RoarDataset-method Man page
totalResults,RoarDatasetMultipleAPA-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/Roar-utils.R
R/RoarDataset-accessors.R
R/RoarDatasetMultipleAPA-accessors.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/roar.R
inst/doc/roar.Rnw
inst/doc/roar.pdf
inst/examples
inst/examples/apa.gtf
inst/examples/roarWrapper.R
inst/examples/roarWrapper_chrBychr.R
inst/examples/roarWrapper_multipleAPA.R
inst/examples/roarWrapper_multipleAPA_bf.R
inst/examples/roarWrapper_multipleAPA_chrBychr.R
inst/examples/roarWrapper_paired_chrBychr.R
man
man/RoarDataset-class.Rd
man/RoarDataset-constructor.Rd
man/RoarDatasetFromFiles-constructor.Rd
man/RoarDatasetMultipleAPA-class.Rd
man/RoarDatasetMultipleAPA-constructor.Rd
man/RoarDatasetMultipleAPAFromFiles-constructor.Rd
man/checkStep-method.Rd
man/combineFisherMethod-method.Rd
man/computePairedPvals-method.Rd
man/computePvals-method.Rd
man/computeRoars-method.Rd
man/cores-method.Rd
man/countPrePost-method.Rd
man/countResults-method.Rd
man/fpkmResults-method.Rd
man/getFisher-method.Rd
man/meanAcrossAssays-method.Rd
man/pvalueCorrectFilter-method.Rd
man/pvalueFilter-method.Rd
man/roar-package.Rd
man/standardFilter-method.Rd
man/totalResults-method.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_roar.R
tests/testthat/test_roar_multipleAPA.R
tests/testthat/test_roar_results.R
vignettes
vignettes/prepost.pdf
vignettes/roar.Rnw
vignettes/roar.bib
roar documentation built on May 20, 2017, 10:47 p.m.

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