update master to 0.99.2 #116
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70 persistent cache
match workflow name to master branch workflow name
Jtm remove vestigial documentation
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Modular functions are not ready for the dev version of the package. They are still being worked on in the assemble_modular_create_domino branch
Differential domino testdata
paste() within condition signal functions is redundant because the functions already coerce the arguments to strings and paste them together in the same procedure as paste0()
This was originally code I had included to diagnose when receptor complexes were not included in the final domino object because a component gene did not meet expression threshold parameters. This is being removed because it substantially clutters the console with receptors present in the database but not expressed in the subject data set, occluding other messages that may be more important for the users' interpretation.
Switch from sapply to vapply uncovered a bug with writing the rl_map where cases in which there are multiple genes associated with a uniprot ID in the CellPhoneDB genes table result in a simplified vector of all the genes being returned in the loop. By setting expectation of a length 1 character vector, we must enforce that a single gene name is returned. We will default to using the first orcurance of a mapped gene. If a more specific solution is required, its up to the user or CellPhoneDB to remove outdated or incorrect uniprot to gene mappings.
This would occur if there were no interactions including a gene annotated as a receptor in the rl_map.
In cases where seq was used to generate a sequence of integers starting at 1, the seq() function was replaced with seq_len() for better expected behaviors for 0 length sequences.
Bioc coding practice notes
dimalvovs
approved these changes
May 3, 2024
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Re-running devtools::document() after incrementing the version number did not change any of the files, so no further commits are needed for the resubmission. |
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