make_se {DEP} | R Documentation |
make_se
creates a SummarizedExperiment object
based on two data.frames: the protein table and experimental design.
make_se(proteins_unique, columns, expdesign)
proteins_unique |
Data.frame,
Protein table with unique names annotated in the 'name' column
(output from |
columns |
Integer vector, Column numbers indicating the columns containing the assay data. |
expdesign |
Data.frame,
Experimental design with 'label', 'condition'
and 'replicate' information.
See |
A SummarizedExperiment object with log2-transformed values.
# Load example data <- UbiLength data <- data[data$Reverse != "+" & data$Potential.contaminant != "+",] data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";") # Make SummarizedExperiment columns <- grep("LFQ.", colnames(data_unique)) exp_design <- UbiLength_ExpDesign se <- make_se(data_unique, columns, exp_design)