Fix conversion fuction #158
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…v/immunedeconv into fix_conversion_fuction
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…v/immunedeconv into fix_conversion_fuction
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…v/immunedeconv into fix_conversion_fuction
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@grst do you have an idea about what's wrong here? I assumed we needed to update the version of conda but this looks already like the latest one |
…v/immunedeconv into fix_conversion_fuction
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…v/immunedeconv into fix_conversion_fuction # Conflicts: # .github/workflows/conda.yml
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@grst I'm waiting to merge to see what you think about that |
| @@ -29,7 +29,7 @@ custom_deconvolution_methods <- c( | |||
| "EPIC" = "epic", | |||
| "CIBERSORT" = "cibersort", | |||
| "ConsensusTME" = "consensus_tme", | |||
| "BASE" = "base" | |||
| "seqImmuCC" = "seqimmucc" | |||
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Removing a method is a breaking change that should only happen with a good reason (+ major version bump + explanation in changelog)
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I'm not removing a method here, I'm just removing the possibility to use it with a custom matrix (this is due to an error in my implementation)
R/immune_deconvolution_methods.R
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| rownames <- Reduce(intersect, lapply(list.results, rownames)) | ||
| list.results <- lapply(list.results, function(x) x[rownames, ]) |
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Why? And wouldn't you rather want an "outer" join with NAs (or 0s) in places where individual samples don't have a cell-type?
Maybe add a comment, why this was necessary to understand this better in the future.
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Could be another solution too
| @@ -124,26 +124,28 @@ In addition, human-based methods can be used to deconvolute mouse data through t | |||
| to the corresponding human orthologues | |||
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| ```R | |||
| gene_expression_matrix <- immunedeconv::mouse_genes_to_human(gene_expression_matrix) | |||
| gene_expression_matrix <- immunedeconv::convert_human_mouse_genes(gene_expression_matrix, convert_to = "human") | |||
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Did I get this right that the function wasn't renamed, but just the wrong function reference from the tutorial?
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The function was renamed because instead of going from mouse genes to human, now it can go both ways
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This is also a breaking change then... Usually what is done in such cases is to keep the old function as an alias to the new one (provided that it has a compatible signature) and show a deprecation warning when it is still used.
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…v/immunedeconv into fix_conversion_fuction
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Update of conversion function between mouse and human genes
Addition of custom deconvolution with seqimmucc
Fixing minor bugs (#156 )