anota2seqGetThresholds: Get filtering criteria thresholds

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

Description

Get the filtering criteria used for the anota2seqSelSigGenes function.

Usage

anota2seqGetThresholds(object, analysis, selContrast)

## S4 method for signature 'Anota2seqDataSet'
anota2seqGetThresholds(object, analysis, 
  selContrast)

Arguments

object	An Anota2seqDataSet.
analysis	A vector containing "translated mRNA", "total mRNA", "translation" or "buffering" specifying for which analysis the selected thresholds should 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 list with the filtering criteria applied when filtering the anota2seqAnalyze output using the anota2seqSelSigGenes function. For details on filtering criteria see anota2seqSelSigGenes function help.

See Also

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 thresholds
thresholds <- anota2seqGetThresholds(Anota2seqDataSet,
                                       analysis = "translation",
                                       selContrast = 1)

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