anota2seqGetDeltaData: Accessor for the fold changes and TE scores stored in the...

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

Description

anota2seqAnalyze, anota2seqSelSigGenes and anota2seqRun calculate the fold change values of translated mRNA (e.g. polysome-associated mRNA or RPFs) and total mRNA. They also provide deltaPT which is the mean log2(translated mRNA data / total mRNA data) between treatments difference (also referred to as translational efficiency (TE) scores) and similarly deltaTP log2(total mRNA data/translated mRNA data). anota2seqGetDeltaData allows access these delta data that can be useful for plotting or custom filtering.

Usage

anota2seqGetDeltaData(object, output, analysis, selContrast)

## S4 method for signature 'Anota2seqDataSet'
anota2seqGetDeltaData(object, output, analysis, 
  selContrast)

Arguments

object	An Anota2seqDataSet. Should contain the output of the anota2seqAnalyze function (and of anota2seqSelSigGenes if the output parameter is set to "selected", see below).
output	A character string specifying whether the deltaData output of the anota2seqAnalyze ("full", this will output deltaData for all genes) or of the anota2seqSelSigGenes ("selected", this will output deltaData for selected genes only) function should be returned.
analysis	A character to specify for which analysis you want to retrieve the deltaData. Can be "translated mRNA", "total mRNA", "translation" or "buffering". Depending on the analysis parameter the returned deltaData will be influenced, i.e. when analysis is set to "total mRNA" a deltaT column will be returned, when analysis is set to "translated mRNA" a deltaP column will be returned; if analysis is set to "translation" a matrix with deltaP and deltaPT will be returned, if analysis is set to "buffering" a matrix with deltaT and deltaTP will be returned.
selContrast	A numeric vector specifying for which contrast the output should be retrieved. The contrast number corresponds to the position of the column in the automatically generated or specified contrast matrix.

Value

A matrix containing rows for all identifiers for the specified analysis and contrast. The matrix contains the following columns depending on analysis:

• deltaP: log2 fold change of translated mRNA across treatments (e.g. polysome-associated mRNA or RPF)

• deltaT: log2 fold changes of total mRNA across treatments,

• deltaPT: mean log2(translated mRNA data / total mRNA data) between treatments difference

• deltaTP: mean log2(total mRNA data / translated mRNA data) between treatments difference

When analysis is "translated mRNA" the matrix contains deltaP. When analysis is "total mRNA" the matrix contains deltaT. When analysis is "translation" the matrix contains deltaP and deltaPT. When analysis is "buffering" the matrix contains deltaT and deltaTP.

See Also

anota2seqAnalyze, anota2seqSelSigGenes

Examples

data(anota2seq_data)
# Initialize Anota2seqDataSet
Anota2seqDataSet <- anota2seqDataSetFromMatrix(
    dataP = anota2seq_data_P[1:100,],
    dataT = anota2seq_data_T[1:100,],
    phenoVec = anota2seq_pheno_vec,
    dataType = "RNAseq",
    normalize = TRUE)
# Run analysis of differential translation
Anota2seqDataSet <- anota2seqAnalyze(Anota2seqDataSet, 
                                     analysis = "translation")
# Run anota2seqSelSigGenes 
Anota2seqDataSet <- anota2seqSelSigGenes(Anota2seqDataSet, 
                                         analysis="translation", 
                                         selContrast = 1,
                                         maxPAdj = .15)

# Get delta data
delta_translation <- anota2seqGetDeltaData(Anota2seqDataSet,
                                             output = "selected",
                                             analysis = "translation",
                                             selContrast = 1)

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