pxFileTypes: Infer file type

In lgatto/rpx: R Interface to the ProteomeXchange Repository

Infer file type

Description

The pxFileTypes() function inferres mass spectrometry and proteomics file types based on a currated table of file types and associated patterns. This table can be accessed with fileTypes(). See the examples below for the content and format of the table.

The types of the files in a PXDataset object can be accessed with the pxfiles(as.vector = FALSE) function. See examples in the pxfiles() manual page.

updatePxFileTypes() updates the file types of a PXDataset instance using pxFileTypes(). This function also udpates the cached object unless cache is set to NULL. This function is useful to harmonise file types when the data in fileTypes() is updated.

The file types table is generated by scripts/make_fileTypes.R.

Usage

fileTypes()

pxFileTypes(fls, types = fileTypes())

updatePxFileTypes(object, cache = rpxCache())

Arguments

fls	character() of file names whose types need to be inferred based on their file extenstion.
types	data.frame of file types. Default is fileTypes().
object	Object of class PXDataset.
cache	Object of class BiocFileCache.

Value

A data.frame with the filenames and their inferred types.

Author(s)

Laurent Gatto with contributions via mastodon from Dr. Samuel Wein, Michael MacCoss, Marc Vaudel, Phil Wilmarth and Dave Tabb to identify several file types (see inst/make_file_types.R for details).

References

• McDonald, W. et al. 2004. "MS1, MS2, and SQT-Three Unified, Compact, and Easily Parsed File Formats for the Storage of Shotgun Proteomic Spectra and Identifications." Rapid Communications in Mass Spectrometry 18 (18):2162–68.

• Deutsch, Eric W. 2012. "File Formats Commonly Used in Mass Spectrometry Proteomics." Molecular & Cellular Proteomics 11 (12):1612–21.

• File formats in PRIDE Archive: https://www.ebi.ac.uk/pride/markdownpage/pridefileformats.

Examples

fileTypes()

pxFileTypes("foo")
pxFileTypes("foo.mzML")
pxFileTypes("foo.raw")
pxFileTypes("foo.txt")
pxFileTypes("foo.R")
pxFileTypes("foo.fasta")

pxFileTypes(c("foo", "foo.mzML", "foo.R", "foo.fasta"))

lgatto/rpx documentation built on Oct. 2, 2023, 9:15 p.m.