generateAnnotatedMatrix: Generate an annotated data frame from statistics object

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

Generate an annotated data frame from statistics object

Description

Extracts key values (p-value, adjusted p-value, log2-fold change and average expression values) from an NormalyzerStatistics instance and appends these to the annotation- and data-matrices

Usage

generateAnnotatedMatrix(nst, prefixSep = "_", compLabels = NULL)

Arguments

nst	NormalyzerDE statistics object.
prefixSep	Character string for separating the prefix names from the statistics suffix
compLabels	Vector containing strings to use as prefix for statistical comparisons

Value

outDf Annotated statistics matrix

Examples

data(example_stat_summarized_experiment)
statObj <- NormalyzerStatistics(example_stat_summarized_experiment)
statObj <- calculateContrasts(statObj, comparisons=c("1-2", "2-3"), condCol="group", type="limma")
annotDf <- generateAnnotatedMatrix(statObj)

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