make_se_parse {DEP} | R Documentation

## Data.frame to SummarizedExperiment object conversion using parsing from column names

### Description

`make_se_parse` creates a SummarizedExperiment object based on a single data.frame.

### Usage

    make_se_parse(proteins_unique, columns, mode = c("char", "delim"),
      chars = 1, sep = "_")

### 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.
`mode` | "char" or "delim", The mode of parsing the column headers. "char" will parse the last number of characters as replicate number and requires the 'chars' parameter. "delim" will parse on the separator and requires the 'sep' parameter.
`chars` | Numeric(1), The number of characters to take at the end of the column headers as replicate number (only for mode == "char").
`sep` | Character(1), The separator used to parse the column header (only for mode == "delim").

### 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))
    se <- make_se_parse(data_unique, columns, mode = "char", chars = 1)
    se <- make_se_parse(data_unique, columns, mode = "delim", sep = "_")

[Package DEP version 1.12.0 Index]