calculateContrasts: Performs statistical comparisons between the supplied...

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

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.

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")

ComputationalProteomics/NormalyzerDE documentation built on Sept. 18, 2023, 9:15 p.m.