calculateContrasts {NormalyzerDE} | R Documentation |
Optionally, a batch column can be specified allowing compensation for covariate variation in the statistical model. This is only compatible with a Limma-based statistical analysis.
calculateContrasts( nst, comparisons, condCol, batchCol = NULL, splitter = "-", type = "limma", leastRepCount = 1 ) ## S4 method for signature 'NormalyzerStatistics' calculateContrasts( nst, comparisons, condCol, batchCol = NULL, splitter = "-", type = "limma", leastRepCount = 1 )
nst |
Results evaluation object. |
comparisons |
String with comparisons for contrasts. |
condCol |
Column name in design matrix containing condition information. |
batchCol |
Column name in design matrix containing batch information. |
splitter |
Character dividing contrast conditions. |
type |
Type of statistical test (Limma or welch). |
leastRepCount |
Least replicates in each group to be retained for contrast calculations |
nst Statistics object with statistical measures calculated
data(example_stat_summarized_experiment) nst <- NormalyzerStatistics(example_stat_summarized_experiment) results <- calculateContrasts(nst, c("1-2", "2-3"), "group") resultsBatch <- calculateContrasts(nst, c("1-2", "2-3"), "group", batchCol="batch")