Change how get_gene_expression handle duplications
#59
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This commit also fixes an error in the creation of multi_exp column (sample_id replaced by sample_seqType in the split call) and changes how duplications are handled.
rdmorin
reviewed
May 2, 2024
| stopifnot("You did not specify a valid engine. Please use one of \"read_tsv\", \"grep\", \"vroom\", or \"fread\"." = | ||
| engine %in% c("read_tsv", "grep", "vroom", "fread")) | ||
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| if(default_priority & !missing(prioritize_rows_by)){ |
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These three lines need to be removed. I think these were left over from the earlier implementation that was recently scrapped.
rdmorin
reviewed
May 2, 2024
| @@ -231,52 +221,39 @@ get_gene_expression = function(these_samples_metadata, | |||
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| # add column `multi_exp` to inform whether there are more than one | |||
| # `mrna_sample_id` associated to a `sample_id` | |||
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It seems like the whole expression data set is loaded in before anything is done with the metadata. This seems wasteful but perhaps it's a limitation imposed by having some of the required information exist only in the expression table?
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In this PR, I added the parameter
default_priorityfor default row prioritization. The default I'm using is:Please, let me know whether there is a more adequate default prioritization.