import_IsobarQuant {DEP} | R Documentation

## Import from IsobarQuant

### Description

`import_IsobarQuant` imports a protein table from IsobarQuant and converts it into a SummarizedExperiment object.

### Usage

    import_IsobarQuant(proteins, expdesign, intensities = "signal_sum",
      names = "gene_name", ids = "protein_id", delim = "[|]")

### Arguments

`proteins` | Data.frame, Protein table for which unique names will be created.
`expdesign` | Data.frame, Experimental design with 'label', 'condition' and 'replicate' information. See `UbiLength_ExpDesign` for an example experimental design.
`intensities` | Character(1), Prefix of the columns containing sample intensities.
`names` | Character(1), Name of the column containing feature names.
`ids` | Character(1), Name of the column containing feature IDs.
`delim` | Character(1), Sets the delimiter separating the feature names within on protein group.

### Value

A SummarizedExperiment object with log2-transformed values and "name" and "ID" columns containing unique names and identifiers.

### Examples

    ## Not run:
    # Load data
    isobarquant_table <- read.csv("testfile.txt", header = TRUE,
                                  stringsAsFactors = FALSE, sep = "\t")
    exp_design <- read.csv("test_experimental_design.txt", header = TRUE,
                                  stringsAsFactors = FALSE, sep = "\t")
    # Import data
    se <- import_IsobarQuant(isabarquant_table, exp_design)

    ## End(Not run)

[Package DEP version 1.12.0 Index]