extract_msraw_data: Read a bunch of mzXML files to acquire their metadata.

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

Read a bunch of mzXML files to acquire their metadata.

Description

I have had difficulties getting the full set of correct parameters for a DDA/DIA experiment. After some poking, I eventually found most of these required prameters in the mzXML raw files. Ergo, this function uses them. 20190310: I had forgotten about the mzR library. I think much (all?) of this is redundant with respect to it and perhaps should be removed in deference to the more complete and fast implementation included in mzR.

Usage

extract_msraw_data(
  metadata,
  write_windows = TRUE,
  id_column = "sampleid",
  file_column = "raw_file",
  allow_window_overlap = FALSE,
  start_add = 0,
  format = "mzXML",
  parallel = TRUE,
  savefile = NULL,
  ...
)

Arguments

metadata	Data frame describing the samples, including the mzXML filenames.
write_windows	Write out SWATH window frames.
id_column	What column in the sample sheet provides the ID for the samples?
file_column	Which column in the sample sheet provides the filenames?
allow_window_overlap	What it says on the tin, some tools do not like DIA windows to overlap, if TRUE, this will make sure each annotated window starts at the end of the previous window if they overlap.
start_add	Another strategy is to just add a static amount to each window.
format	Currently this handles mzXML or mzML files.
parallel	Perform operations using an R foreach cluster?
savefile	If not null, save the resulting data structure to an rda file.
...	Extra arguments, presumably color palettes and column names and stuff like that.

Value

List of data extracted from every sample in the MS run (DIA or DDA).

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