-
Notifications
You must be signed in to change notification settings - Fork 8
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Cleanup utility functions #164
Conversation
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. |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
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?
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
No, it's not used at all.
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.tables
create_feature_sample_table
plot_rt_histograms
sort_samples_by_acquisition_number
recover_weaker
totwo.step.hybrid.R
as_wide_aligned_table
totwo.step.hybrid.R
extract_pattern_colnames
totwo.ste.hybrid.R
long_to_wide_feature_table
(and vice versa) totwo.step.hybrid.R
pivot_feature_values
totwo.step.hybrid.R
recover_weaker_signals
totwo.step.hybrid.R
find_mz_match
tohybrid.R
as_feature_crosstab
totwo.step.hybrid.R
two.step.hybrid.R
as obsolete