extract_mzML_scans: Parse a mzML file and return the relevant data.

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

Parse a mzML file and return the relevant data.

Description

This does the actual work for extract_scan_data(). This levers mzR to provide the data and 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).

Usage

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

Arguments

file	Input mzML 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.

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.