importBrukerXmassImg: Import a MSI dataset from Bruker XMASS folder and a XML file.

Description Usage Arguments

View source: R/ImportBrukerXMASSImage.R

Description

This function converts MSI data contained in Bruker XMASS directory into rMSI data structure. Only spectra contained in the XML file are imported. The ramdisk will be created at the specified directory as a collection of ff files with the maximum specified size (50 MB is the default setting). The rMSI object pointing to ramdisk and containing RAM stored variables is returned.

Usage

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importBrukerXmassImg(
  raw_data_full_path,
  resolution_um,
  xml_file_full_path,
  txt_spectrum_path = NULL,
  selected_img = 1,
  ...
)

Arguments

raw_data_full_path

Where the Bruker XMASS data is located.

resolution_um

The image pixel size un micrometers (sorry it can not be read directly from XMASS).

xml_file_full_path

Full path to the XML file or alternatively an already parsed xml list resulting from ParseBrukerXML() function.

txt_spectrum_path

Full path to a bruker spectrum txt file to extract mass axis (optional).

selected_img

the image number to select in the XML file containing various classes.

...

Extra parameters to .readBrukerXmassImg ( for example max_ff_file_size_MB as max size in MB of each ff file of the ramdisk).


prafols/rMSI documentation built on Dec. 12, 2021, 7:29 p.m.