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RECETOX / recetox-aplcms

This is a custom fork of apLCMS containing adaptations for large scale studies.
GNU General Public License v2.0
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Ensure the tool also works with all formats compatible with mzR #185

Closed hechth closed 6 months ago

hechth commented 1 year ago

mzR support mzXML and mzdata formats - it would be nice to also implement the package to natively be able to deal with those formats.

This should be implemented in this function: https://github.com/RECETOX/recetox-aplcms/blob/master/R/load.lcms.R

This should actually first be tested with which formats it already works using this file (https://github.com/RECETOX/recetox-aplcms/blob/master/tests/testdata/mbr_test0_copy.mzml) and converting it to mzXML and mzData formats using proteowizard (msconvert in galaxy).

wverastegui commented 7 months ago

The function load.lcms.R supports mzXML format. However, it could not be tested with mzData format since msconvert does not offer conversion to mzData.

hechth commented 6 months ago

This should be implemented as a unit test within the package using the mzXML and mzData files.

hechth commented 6 months ago

For testing with mzdata you can use the file available here and add it to the remote-files text files which contain the URLs.

https://gitlab.ics.muni.cz/umsa/umsa-files/-/blob/master/testdata/recetox-aplcms/input/alg3.mzdata?ref_type=heads