Package: roar 1.49.0

Elena Grassi

roar: Identify differential APA usage from RNA-seq alignments

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

Authors:Elena Grassi

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
roar/json (API)

# Install 'roar' in R:

install.packages('roar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vodkatad/roar/issues

On BioConductor:roar-1.49.0(bioc 3.24)roar-1.48.0(bioc 3.23)

sequencing highthroughputsequencing rnaseq transcription

5.05 score 4 stars 14 scripts 2 mentions 14 exports 51 dependencies

Last updated from:ea42a9ed24. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	197
linux-devel-x86_64	NOTE	409
source / vignettes	OK	381
linux-release-x86_64	NOTE	369
macos-release-arm64	NOTE	201
macos-oldrel-arm64	NOTE	228
windows-devel	NOTE	267
windows-release	NOTE	272
windows-oldrel	NOTE	302
wasm-release	OK	150

Exports:computePairedPvals computePvals computeRoars countPrePost countResults fpkmResults pvalueCorrectFilter pvalueFilter RoarDataset RoarDatasetFromFiles RoarDatasetMultipleAPA RoarDatasetMultipleAPAFromFiles standardFilter totalResults

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys UCSC.utils XML XVector yaml

Identify differential APA usage from RNA-seq alignments

Introduction | Input data | Analysis steps | Appendix

Rendered fromroar.Rnwusingutils::Sweave

Last update: 2017-11-27
Started: 2013-12-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Identify differential APA usage from RNA-seq alignments	roar-package roar
Private/inner/helper method to check the order of the invoked analysis methods	checkStep
Private/inner/helper method to combine pvalues of independent test with the Fisher method	combineFisherMethod
Computes pvalues (Fisher test) on the read counts in this roar analysis	computePairedPvals computePairedPvals, RoarDataset computePairedPvals, RoarDatasetMultipleAPA
Computes pvalues (Fisher test) on the read counts in this roar analysis	computePvals computePvals, RoarDataset computePvals, RoarDatasetMultipleAPA
Computes m/M and roar values	computeRoars computeRoars, RoarDataset, numeric, numeric computeRoars, RoarDatasetMultipleAPA, numeric, numeric
Method to check how many cores are used by a roar analysis - right now not useful	cores
Counts reads falling over PRE/POST portions of the given transcripts	countPrePost countPrePost,RoarDataset,logical countPrePost,RoarDatasetMultipleAPA
Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object	countResults countResults, RoarDataset countResults, RoarDatasetMultipleAPA
Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object	fpkmResults fpkmResults, RoarDataset fpkmResults, RoarDatasetMultipleAPA
Private/inner/helper method to perform Fisher test	getFisher
Private/inner/helper method to get average counts across samples	meanAcrossAssays
Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object	pvalueCorrectFilter pvalueCorrectFilter, RoarDataset pvalueCorrectFilter, RoarDatasetMultipleAPA
Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object	pvalueFilter pvalueFilter, RoarDataset pvalueFilter, RoarDatasetMultipleAPA
Creates a 'RoarDataset' object	RoarDataset
Class '"RoarDataset"'	computePairedPvals,RoarDataset,numeric,numeric-method computePvals,RoarDataset-method computeRoars,RoarDataset-method cores,RoarDataset-method countPrePost,RoarDataset,logical-method countPrePost,RoarDataset-method countResults,RoarDataset-method fpkmResults,RoarDataset-method pvalueCorrectFilter,RoarDataset,numeric,numeric,character-method pvalueFilter,RoarDataset,numeric,numeric-method RoarDataset-class standardFilter,RoarDataset,numeric-method totalResults,RoarDataset-method
Creates a 'RoarDataset' object	RoarDatasetFromFiles
Creates a 'RoarDatasetMultipleAPA' object	RoarDatasetMultipleAPA
Class '"RoarDatasetMultipleAPA"'	computePairedPvals,RoarDatasetMultipleAPA,numeric,numeric-method computePvals,RoarDatasetMultipleAPA-method computeRoars,RoarDatasetMultipleAPA-method cores,RoarDatasetMultipleAPA-method countPrePost,RoarDatasetMultipleAPA,logical-method countPrePost,RoarDatasetMultipleAPA-method countResults,RoarDatasetMultipleAPA-method fpkmResults,RoarDatasetMultipleAPA-method pvalueCorrectFilter,RoarDatasetMultipleAPA,numeric,numeric,character-method pvalueFilter,RoarDatasetMultipleAPA,numeric,numeric-method RoarDatasetMultipleAPA-class standardFilter,RoarDatasetMultipleAPA,numeric-method totalResults,RoarDatasetMultipleAPA-method
Creates a 'RoarDatasetMultipleAPA' object	RoarDatasetMultipleAPAFromFiles
Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object	standardFilter standardFilter, RoarDataset standardFilter, RoarDatasetMultipleAPA
Returns a dataframe with results of the analysis for a 'RoarDataset' or a 'RoarDatasetMultipleAPA' object	totalResults totalResults, RoarDataset totalResults, RoarDatasetMultipleAPA