readMgf: Reading MGF files

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

Reading MGF files

Description

The readMgf() function imports the data from a file in MGF format reading all specified fields and returning the data as a S4Vectors::DataFrame().

For very large MGF files the readMgfSplit() function might be used instead. In contrast to the readMgf() functions, readMgfSplit() reads only nlines lines from an MGF file at once reducing thus the memory demand (at the cost of a lower performance, compared to readMgf()).

Usage

readMgf(
  f,
  msLevel = 2L,
  mapping = spectraVariableMapping(MsBackendMgf()),
  annotated = FALSE,
  ...,
  BPPARAM = SerialParam()
)

readMgfSplit(
  f,
  msLevel = 2L,
  mapping = spectraVariableMapping(MsBackendMgf()),
  nlines = 1e+05,
  BPPARAM = SerialParam(),
  ...
)

Arguments

f	character(1) with the path to an mgf file.
msLevel	numeric(1) with the MS level. Default is 2.
mapping	named character vector to rename mgf fields to spectra variables.
annotated	For readMgf(): logical(1) whether the MGF file contains additional peak annotations. See examples below or the documentation for MsBackendAnnotatedMgf() for information on the expected format.
...	Additional parameters, currently ignored.
BPPARAM	parallel processing setup that should be used. Only the parsing of the imported MGF file is performed in parallel.
nlines	for readMgfSplit(): integer(1) with the number of lines that should be imported and parsed in each iteration.

Value

A DataFrame with each row containing the data from one spectrum in the MGF file. m/z and intensity values are available in columns "mz" and "intensity" in a list representation. For readMgf() with annotated = TRUE also all peaks annotation columns (named ⁠"V1", etc) are provided in a list representation, with the lengths of elements matching those of ⁠"mz"or"intensity"'.

Author(s)

Laurent Gatto, Johannes Rainer, Sebastian Gibb, Corey Broeckling

Examples

fls <- dir(system.file("extdata", package = "MsBackendMgf"),
    full.names = TRUE, pattern = "mgf$")[1L]

readMgf(fls)

## Annotated MGF
fl <- system.file("extdata", "xfiora.mgf", package = "MsBackendMgf")
res <- readMgf(fl, annotated = TRUE)
colnames(res)
res$V1

rformassspectrometry/MsBackendMgf documentation built on June 12, 2025, 12:32 a.m.