This PR allows us to use the auto.merge option for fastMNN integration, and also allows for users to provide a character vector of library ids to use as the order for integration.
What changes did you make?
The following modifications were made to the perform-integration.R script:
The --fastmnn_auto_merge argument added (default is currently false, but will be set to true using the config.yaml file to set the argument in the snakemake workflow in an upcoming PR)
The fastmnn_merge_order argument added and logic to use this list when provided (only if --fastmnn_auto_merge is set to false, otherwise this argument will be NULL)
Were there any other solutions that you tried?
The formatting of the fastmnn_merge_order at line 108 was implemented because without this, I receive the following error:
Error in .create_tree_predefined(batches, restrict, merge.order) :
invalid leaf nodes specified in 'merge.order'
Otherwise, users would need to use c("library02", "library01") when implementing this argument.
Any comments, concerns, or questions important for reviewers
Does this PR correctly address what's noted on issue #347?
Checklist
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Issue Addressed Closes #347
What is the purpose of these changes?
This PR allows us to use the
auto.mergeoption for fastMNN integration, and also allows for users to provide a character vector of library ids to use as the order for integration.What changes did you make?
The following modifications were made to the
perform-integration.Rscript:--fastmnn_auto_mergeargument added (default is currently false, but will be set to true using theconfig.yamlfile to set the argument in the snakemake workflow in an upcoming PR)fastmnn_merge_orderargument added and logic to use this list when provided (only if--fastmnn_auto_mergeis set to false, otherwise this argument will be NULL)Were there any other solutions that you tried?
The formatting of the
fastmnn_merge_orderat line 108 was implemented because without this, I receive the following error:Otherwise, users would need to use
c("library02", "library01")when implementing this argument. Any comments, concerns, or questions important for reviewersChecklist
Place an
xin all boxes that you have completed.