Anota2seqDataSet-class: Anota2seqDataSet class

In ChrOertlin/anota2seq: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Description

A S4 class to store and collect output from the anota2seq workflow.

Details

The Anota2seqDataSet will be used to collect outputs of the anota2seqPerformQC, anota2seqResidOutlierTest,anota2seqAnalyze, anota2seqSelSigGenes and anota2seqRegModes functions. The results that are collected in the Anota2seqDataSet can be accessed using the anota2seq.get methods. Furthermore show() gives an overview of the stored objects in the Anota2seqDataSet.

Slots

dataT

a matrix containing normalized data for total mRNA. Can be accessed using anota2seqGetNormalizedData.

dataP

a matrix containing normalized data for translated mRNA. Can be accessed using anota2seqGetNormalizedData.

phenoVec

a vector describing the sample class for each column of dataT and dataP. Can be accessed using anota2seqGetCovariates.

batchVec

an optional vector describing a batch class for each column of dataT and dataP. Can be accessed using anota2seqGetCovariates.

contrasts

a matrix describing the contrasts to be used in the analysis. Can be accessed using anota2seqGetContrasts.

qualityControl

after running anota2seqPerformQC, its output will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetQualityControl.

residOutlierTest

after running anota2seqResidOutlierTest, its output will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetResidOutlierTest.

translatedmRNA

after running anota2seqAnalyze with analysis parameter set to "translated mRNA" (or anota2seqRun), its output (results of the differential expression analysis) will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetOutput with analysis = "translated mRNA" and output = "full".

totalmRNA

after running anota2seqAnalyze with analysis parameter set to "total mRNA" (or anota2seqRun), its output (results of the differential expression analysis) will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetOutput with analysis = "total mRNA" and output = "full".

translation

after running anota2seqAnalyze with analysis parameter set to "translation" (or anota2seqRun), its output (results of the analysis of changes in translational efficiency leading to altered protein levels) will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetOutput with analysis = "translation" and output = "full".

buffering

after running anota2seqAnalyze with analysis parameter set to "buffering" (or anota2seqRun), its output (results of the analysis of changes in translational efficiency leading to buffering) will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetOutput with analysis = "buffering" and output = "full".

selectedTranslatedmRNA

after running anota2seqSelSigGenes with analysis parameter set to "translated mRNA" (or anota2seqRun), its output (results of the differential expression analysis on selected genes based on user defined thresholds in anota2seqSelSigGenes) will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetOutput with analysis = "translated mRNA" and output = "selected".

selectedTotalmRNA

after running anota2seqSelSigGenes with analysis parameter set to "total mRNA" (or anota2seqRun), its output (results of the differential expression analysis on selected genes based on user defined thresholds in anota2seqSelSigGenes) will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetOutput with analysis = "total mRNA" and output = "selected".

selectedTranslation

after running anota2seqSelSigGenes with analysis parameter set to "translation" (or anota2seqRun), its output (results of the analysis of changes in translational efficiency leading to altered protein levels on selected genes) will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetOutput with analysis = "translation" and output = "selected".

selectedBuffering

after running anota2seqSelSigGenes with analysis parameter set to "buffering" (or anota2seqRun), its output (results of the analysis of changes in translational efficiency leading to buffering on selected genes) will be saved in this slot of the Anota2seqDataSet object. Can be accessed using anota2seqGetOutput with analysis = "buffering" and output = "selected".

mRNAAbundance

after running anota2seqRegModes (or anota2seqRun), its output will be saved in this slot of the Anota2seqDataSet object. This output will contains results of the differential expression analysis on genes selected to be considered as regulated by mRNA abundance. The definition of regulation by mRNA abundance can be based on results from total mRNA, translated mRNA or both (this is set by the user on parameter mRNASelect in anota2seqRegModes). Statistics results from mRNA type(s) considered in this definition will be saved in this slot. Can be accessed using anota2seqGetOutput with analysis = "mRNA abundance" and output = "selected".

deltaData

after running anota2seqAnalyze, an additional output called deltaData will be stored in the Anota2seqDataSet. deltaData is a list of matrices with one deltaData matrix for each contrast. For each matrix the rows correspond to the mRNA in the dataset and has the following columns: deltaP, deltaT, deltaPT and deltaTP. deltaP is translated mRNA fold change, deltaT is the total mRNA fold change, deltaPT is the within contrast difference difference of the log ratios with translated mRNA in the nominator and total mRNA in the denominator (deltaPT is commonly called TE score = Translational efficiency score) and deltaTP is the within contrast difference of the log ratios with total mRNA in the nominator and translated mRNA in the denominator.

ChrOertlin/anota2seq documentation built on Aug. 4, 2021, 2:17 p.m.