Cleanup utility functions #164
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maximskorik
approved these changes
Nov 24, 2022
hechth
approved these changes
Nov 25, 2022
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| function(metabolite.table, adduct.table, ion.mode="+") | ||
| ### the metabolite.table should be a four-column data frame. The columns should be chemical formula, HMDB_ID, KEGG ID, and monoisotopic mass | ||
| ### The two IDs can be substitute by others | ||
| ### the adduct table should be a four-column data frame. The columns are adduct type, mass divider (absolute value of the number of charges), mass addition (after dividing), and charge of the ion form. |
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This functionality is actually also in some way implemented in recetox-xmsannotator - is it really not needed in this repository? Was it for sure not somehow used in the hybrid?
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This PR is part of #159 with focus on removing obsolete functions and moving some utility functions to a more suitable locations. In particular, it covers the following changes:
make.known.tablescreate_feature_sample_tableplot_rt_histogramssort_samples_by_acquisition_numberrecover_weakertotwo.step.hybrid.Ras_wide_aligned_tabletotwo.step.hybrid.Rextract_pattern_colnamestotwo.ste.hybrid.Rlong_to_wide_feature_table(and vice versa) totwo.step.hybrid.Rpivot_feature_valuestotwo.step.hybrid.Rrecover_weaker_signalstotwo.step.hybrid.Rfind_mz_matchtohybrid.Ras_feature_crosstabtotwo.step.hybrid.Rtwo.step.hybrid.Ras obsolete