reduceTechnicalReplicates: Remove technical replicates from data and design

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

Remove technical replicates from data and design

Description

Collapses sample values into their average. If only one value is present due to NA-values in other technical replicates, then that value is used.

Usage

reduceTechnicalReplicates(se, techRepColName, sampleColName)

Arguments

se	Summarized experiment where the assay contains the data to be reduced, and the colData the data frame
techRepColName	Technical replicates column name in colData
sampleColName	Sample names column name in colData

Details

Takes a SummarizedExperiment where the data is present as the assay and the colData contains the design conditions. In the design conditions there should be one column with the technical replicate groups and one column containing the sample names

Value

reducedSe Summarized experiment with reduced data

Examples

testData <- as.matrix(data.frame(
    c(1,1,1), 
    c(1,2,1), 
    c(7,7,7), 
    c(7,9,7)))
colnames(testData) <- c("a1", "a2", "b1", "b2")
designDf <- data.frame(
    sample=c("a1", "a2", "b1", "b2"), 
    techrep=c("a", "a", "b", "b"))
se <- SummarizedExperiment::SummarizedExperiment(
    assay=testData,
    colData=designDf
)
statObj <- reduceTechnicalReplicates(se, "techrep", "sample")

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