readMzTabData {MSnbase} | R Documentation

## Read an 'mzTab' file

### Description

This function can be used to create an `"MSnSet"` by reading and parsing an `mzTab` file. The metadata section is always used to populate the `MSnSet`'s `experimentData()@other$mzTab` slot.

### Usage

    readMzTabData(
      file,
      what = c("PRT", "PEP", "PSM"),
      version = c("1.0", "0.9"),
      verbose = isMSnbaseVerbose()
    )

### Arguments

`file` | A `character` with the `mzTab` file to be read in.
`what` | One of `"PRT"`, `"PEP"` or `"PSM"`, defining which of protein, peptide PSMs section should be returned as an `MSnSet`.
`version` | A `character` defining the format specification version of the mzTab file. Default is `"1.0"`. Version `"0.9"` is available of backwards compatibility. See `readMzTabData_v0.9` for details.
`verbose` | Produce verbose output.

### Value

An instance of class `MSnSet`.

### Author(s)

Laurent Gatto

### See Also

See `MzTab` and `MSnSetList` for details about the inners of `readMzTabData`.

### Examples

    testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/1_0-Proteomics-Release/PRIDE_Exp_Complete_Ac_16649.xml-mztab.txt"

    prot <- readMzTabData(testfile, "PRT")

    prot

    head(fData(prot))

    head(exprs(prot))

    psms <- readMzTabData(testfile, "PSM")

    psms

    head(fData(psms))

[Package MSnbase version 2.20.1 Index]