Performs statistical comparisons between the supplied conditions. It uses the design matrix and data matrix in the supplied NormalyzerStatistics object. A column is supplied specifying which of the columns in the design matrix that is used for deciding the sample groups. The comparisons vector specifies which pairwise comparisons between condition levels that are to be calculated.
Source:R/NormalyzerStatistics.R
calculateContrasts.RdOptionally, 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.
Usage
calculateContrasts(
nst,
comparisons,
condCol,
batchCol = NULL,
splitter = "-",
type = "limma",
leastRepCount = 1
)
# S4 method for class 'NormalyzerStatistics'
calculateContrasts(
nst,
comparisons,
condCol,
batchCol = NULL,
splitter = "-",
type = "limma",
leastRepCount = 1
)Arguments
- 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
Examples
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")