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roar (version 1.2.0)

Identify differential APA usage from RNA-seq alignments

Description

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

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Version

Version

1.2.0

License

GPL-3

Issues

2

Pull Requests

0

Stars

4

Forks

0

Maintainer

Elena Grassi

Last Published

February 15th, 2017

Functions in roar (1.2.0)

computePvals

Computes pvalues (Fisher test) for this RoarDataset object
checkStep

Private/inner/helper method to check the order of the invoked analysis methods
combineFisherMethod

Private/inner/helper method to combine pvalues of independent test with the Fisher method
computePairedPvals

Computes pvalues (Fisher test) for this RoarDataset object
cores

Method to check how many cores are used by a roar analysis - right now not useful
getFisher

Private/inner/helper method to perform Fisher test
fpkmResults

Returns a dataframe with results of the analysis for a RoarDataset object
countPrePost

Counts reads falling over PRE/POST portions of the given transcripts
countResults

Returns a dataframe with results of the analysis for a RoarDataset object
computeRoars

Computes m/M and roar values for this RoarDataset object
RoarDatasetFromFiles

Creates a RoarDataset object
totalResults

Returns a dataframe with results of the analysis for a RoarDataset object
meanAcrossAssays

Private/inner/helper method to get average counts across samples
roar-package

Identify differential APA usage from RNA-seq alignments
RoarDataset-class

Class "RoarDataset"