anota2seqGetCovariates: Accessor for the 'phenoVec' and 'batchVec' slots of an...

Description Usage Arguments Value See Also Examples

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

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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

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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"

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