Learn R Programming

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.

Copy Link

Version

Version

1.8.0

License

GPL-3

Issues

2

Pull Requests

0

Stars

4

Forks

0

Maintainer

Elena Grassi

Last Published

February 15th, 2017

Functions in roar (1.8.0)

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

Creates a RoarDataset object
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

Creates a RoarDatasetMultipleAPA object
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

Creates a RoarDataset object
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

Creates a RoarDatasetMultipleAPA object
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"