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roar (version 1.8.0)

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

1.8.0

License

GPL-3

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Maintainer

Elena Grassi

Last Published

February 15th, 2017

Functions in roar (1.8.0)

countResults

Returns a dataframe with results of the analysis for a RoarDataset object or a RoarDatasetMultipleAPA object
cores

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

standardFilter

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

Computes m/M and roar values
RoarDatasetMultipleAPA

countPrePost

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

Returns a dataframe with results of the analysis for a RoarDataset object or a RoarDatasetMultipleAPA object
pvalueFilter

Returns a dataframe with results of the analysis for a RoarDataset object or a RoarDatasetMultipleAPA object
computePvals

Computes pvalues (Fisher test) on the read counts in this roar analysis
computePairedPvals

Computes pvalues (Fisher test) on the read counts in this roar analysis
RoarDataset

combineFisherMethod

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

Private/inner/helper method to get average counts across samples
totalResults

Returns a dataframe with results of the analysis for a RoarDataset or a RoarDatasetMultipleAPA object
getFisher

Private/inner/helper method to perform Fisher test
checkStep

Private/inner/helper method to check the order of the invoked analysis methods
RoarDataset-class

Class "RoarDataset"
RoarDatasetMultipleAPAFromFiles

roar-package

Identify differential APA usage from RNA-seq alignments
pvalueCorrectFilter

Returns a dataframe with results of the analysis for a RoarDataset object or a RoarDatasetMultipleAPA object
RoarDatasetMultipleAPA-class

Class "RoarDatasetMultipleAPA"