0.99.2 update to bioconductor submission #121
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bslib update changed default behavior; manually adding preset
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…/domino2 into krishnan_bslib_pkgdown
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Re-structures the for loop that proceeds through rows of the rl_map using an apply function ending with one call of do.bind(rbind)
initial unit test for parsing rows of rl_maps. Fixes situation where do.call(rbind) of the parsed rows results in the columns of the final data.frame being lists. Addressed by converting the list of lists being bound to a list of data.frames
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 If a more specific solution is required, its up to the user or CellPhoneDB to remove outdated or incorrect uniprot to gene mappings.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
update master to 0.99.2
The prior approach to listing the files did not return an array to FILES (line 6). The new approach immediately lists all files in relevant directories for the bioconductor branch. Files are checked out one at a time in a for loop. Adds bin/bash to the start of the script.
This reverts commit b348b09.
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