make_se {DEP} | R Documentation

## Data.frame to SummarizedExperiment object conversion using an experimental design

### Description

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

### Usage

    make_se(proteins_unique, columns, expdesign)

### 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. See `UbiLength_ExpDesign` for an example experimental design.

### Value

A SummarizedExperiment object with log2-transformed values.

### Examples

    # 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)

[Package DEP version 1.12.0 Index]