extract_mzXML_scans: Parse a mzXML file and return the relevant data.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Parse a mzXML file and return the relevant data.

Description

This does the actual work for extract_scan_data(). When I wrote this function, I had forgotten about the mzR library; with that in mind, this seems to give a bit more information and be a bit faster than my short tests with mzR (note however that my tests were to compare mzR parsing mzML files vs. this function with mzXML, which is a classic apples to oranges).

Usage

extract_mzXML_scans(
  file,
  id = NULL,
  write_acquisitions = TRUE,
  allow_window_overlap = FALSE,
  start_add = 0
)

Arguments

file	Input mzXML file to parse.
id	Chosen ID for the given file.
write_acquisitions	Write acquisition windows.
allow_window_overlap	Some downstream tools cannot deal with overlapping windows. Toggle that here.
start_add	Other downstream tools appear to expect some padding at the beginning of each window. Add that here.

Details

This goes a step further to pull out the windows acquired in the MS/MS scan and print them in formats acceptable to TPP/OpenMS (eg. with and without headers).

Value

The list of metadata, scan data, etc from the mzXML file.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.