anota2seqGetThresholds {anota2seq} | R Documentation

## Get filtering criteria thresholds

### 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)

[Package anota2seq version 1.0.1 Index]