anota2seqGetCovariates {anota2seq} | R Documentation |
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).
anota2seqGetCovariates(object) ## S4 method for signature 'Anota2seqDataSet' anota2seqGetCovariates(object)
object |
An Anota2seqDataSet. |
A list of 2 elements named "phenoVec" and "batchVec" containing the corresponding covariates to be used for the analysis.
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"