anota2seqGetThresholds {anota2seq} | R Documentation |
Get the filtering criteria used for the anota2seqSelSigGenes function.
anota2seqGetThresholds(object, analysis, selContrast) ## S4 method for signature 'Anota2seqDataSet' anota2seqGetThresholds(object, analysis, selContrast)
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. |
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.
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)