anota2seqGetCovariates {anota2seq} | R Documentation

## Accessor for the 'phenoVec' and 'batchVec' slots of an Anota2seqDataSet object.

### Description

Retrieve from an Anota2seqDataSet the covariate(s) to be used in the APV model i.e. the annotation of the samples according to their treatments and batch (when provided).

### Usage

    anota2seqGetCovariates(object)

    ## S4 method for signature 'Anota2seqDataSet'
    anota2seqGetCovariates(object)

### Arguments

`object` | An Anota2seqDataSet.

### Value

A list of 2 elements named "phenoVec" and "batchVec" containing the corresponding covariates to be used for the analysis.

### See Also

`Anota2seqDataSet-class`

### Examples

    data(anota2seq_data)
    # Initialize Anota2seqDataSet
    Anota2seqDataSet <- anota2seqDataSetFromMatrix(
        dataP = anota2seq_data_P[1:100,],
        dataT = anota2seq_data_T[1:100,],
        phenoVec = anota2seq_pheno_vec,
        batchVec = c(1, 2, 3, 4, 1, 2, 3, 4),
        dataType = "RNAseq",
        normalize = TRUE)
    # Run analysis of differential translation
    Anota2seqDataSet <- anota2seqAnalyze(Anota2seqDataSet,
                                         analysis = "translation")
    covariates <- anota2seqGetCovariates(Anota2seqDataSet)
    covariates
    # $phenoVec
    # [1] "ctrl"      "ctrl"      "ctrl"      "ctrl"      "treatment" "treatment"
    # [7] "treatment" "treatment"
    #
    # $batchVec
    # [1] "1" "2" "3" "4" "1" "2" "3" "4"

[Package anota2seq version 1.10.0 Index]