calculateContrasts: Performs statistical comparisons between the supplied...

In NormalyzerDE: Evaluation of normalization methods and calculation of differential expression analysis statistics

Description

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.

Usage

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)

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

Value

nst Statistics object with statistical measures calculated

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")

NormalyzerDE documentation built on Nov. 8, 2020, 8:22 p.m.