MsBackendMgf: MS data backend for mgf files

In michaelwitting/MsBackendMgf: Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files

Description

The MsBackendMgf class supports import and export of MS/MS spectra data from/to files in Mascot Generic Format (mgf) files. After initial import, the full MS data is kept in memory. MsBackendMgf extends the MsBackendDataFrame() backend directly and supports thus the applyProcessing() function to make data manipulations persistent.

New objects are created with the MsBackendMgf function. The backendInitialize method has to be subsequently called to initialize the object and import MS/MS data from (one or more) mgf files.

The MsBackendMgf backend provides an export method that allows to export the data from the Spectra object (parameter x) to a file in mgf format. See the package vignette for details and examples.

Default mappings from fields in the MGF file to spectra variable names are provided by the spectraVariableMapping function. This function returns a named character vector were names are the spectra variable names and the values the respective field names in the MGF files. This named character vector is submitted to the import and export function with parameter mapping. It is also possible to pass own mappings (e.g. for special MGF dialects) with the mapping parameter.

Usage

## S4 method for signature 'MsBackendMgf'
backendInitialize(
  object,
  files,
  mapping = spectraVariableMapping(),
  ...,
  BPPARAM = bpparam()
)

MsBackendMgf()

spectraVariableMapping(format = c("mgf"))

## S4 method for signature 'MsBackendMgf'
export(object, x, file = tempfile(), mapping = spectraVariableMapping(), ...)

Arguments

object	Instance of MsBackendMgf class.
files	character with the (full) file name(s) of the mgf file(s) from which MS/MS data should be imported.
mapping	for backendInitialize and export: named character vector allowing to specify how fields from the MGF file should be renamed. Names are supposed to be the spectra variable name and values of the vector the field names in the MGF file. See output of spectraVariableMapping() for the expected format and examples below or description above for details.
...	Currently ignored.
BPPARAM	Parameter object defining the parallel processing setup to import data in parallel. Defaults to BPPARAM = bpparam(). See bpparam() for more information.
format	for spectraVariableMapping: character(1) defining the format to be used. Currently only format = "mgf" is supported.
x	for export: an instance of Spectra() class with the data that should be exported.
file	character(1) with the (full) file name to which the data should be exported.

Value

See description above.

Author(s)

Laurent Gatto and Johannes Rainer

Examples

library(BiocParallel)
fls <- dir(system.file("extdata", package = "MsBackendMgf"),
    full.names = TRUE, pattern = "mgf$")

## Parallel processing setup: disabling parallel processing by registering
## serial processing. See ?bbparam for details and other options
register(SerialParam())

## Create an MsBackendMgf backend and import data from test mgf files.
be <- backendInitialize(MsBackendMgf(), fls)
be

be$msLevel
be$intensity
be$mz

## The spectra variables that are available; note that not all of them
## have been imported from the MGF files.
spectraVariables(be)

## The variable "TITLE" represents the title of the spectrum defined in the
## MGF file
be$TITLE

## The default mapping of MGF fields to spectra variables is provided by
## the spectraVariableMapping function
spectraVariableMapping()

## We can provide our own mapping e.g. to map the MGF field "TITLE" to a
## variable named "spectrumName":
map <- c(spectrumName = "TITLE", spectraVariableMapping())
map

## We can then pass this mapping with parameter `mapping` to the
## backendInitialize method:
be <- backendInitialize(MsBackendMgf(), fls, mapping = map)

## The title is now available as variable named spectrumName
be$spectrumName

## Next we create a Spectra object with this data
sps <- Spectra(be)

## We can use the 'MsBackendMgf' also to export spectra data in mgf format.
out_file <- tempfile()
export(sps, backend = MsBackendMgf(), file = out_file, map = map)

## The first 20 lines of the generated file:
readLines(out_file, n = 20)

## Next we add a new spectra variable to each spectrum
sps$spectrum_idx <- seq_along(sps)

## This new spectra variable will also be exported to the mgf file:
export(sps, backend = MsBackendMgf(), file = out_file, map = map)
readLines(out_file, n = 20)

michaelwitting/MsBackendMgf documentation built on April 28, 2021, 5:15 a.m.