Data.frame to SummarizedExperiment object conversion using an experimental design

make_se creates a SummarizedExperiment object based on two data.frames: the protein table and experimental design.

Usage

make_se(proteins_unique, columns, expdesign, log2transform = TRUE)

Arguments

proteins_unique

Data.frame, Protein table with unique names annotated in the 'name' column (output from make_unique()).

columns

Integer vector, Column numbers indicating the columns containing the assay data.

expdesign

Data.frame, Experimental design with 'label', 'condition' and 'replicate' information.

log2transform

Logical(1), whether log2 transform the assay, default TRUE.

Value

A SummarizedExperiment object with log2-transformed values.

Examples

# Load example
data(Silicosis_pg)
data <- Silicosis_pg
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

# Make SummarizedExperiment
columns <- grep("LFQ.", colnames(data_unique))

## Load experiement design
data(Silicosis_ExpDesign)
exp_design <- Silicosis_ExpDesign
se <- make_se(data_unique, columns, exp_design)