Uploaded script for Uniprot to ncbi function addresses issue #109 #139
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SunSummoner
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3 tasks
Added functions to map NCBI RefSeq Protein IDs to UniProt Accessions and NCBI Protein Accessions to IPG IDs.
the-mayer
reviewed
Oct 29, 2025
| #' @param uniprot_ids A character vector of UniProt accession IDs. | ||
| #' @return A tibble with UniProt IDs and mapped NCBI accessions. | ||
| #' @examples | ||
| #' up2ncbi_fast(c("P12345", "Q9Y263")) |
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update example to match exported function name
the-mayer
reviewed
Oct 29, 2025
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| library(httr2) | ||
| library(dplyr) | ||
| library(purrr) |
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remove library calls function. instead, import necessary functions with roxygen @importFrom comments
the-mayer
reviewed
Oct 29, 2025
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| if (!requireNamespace("rentrez", quietly = TRUE)) { | ||
| stop("Please install 'rentrez' with install.packages('rentrez') or BiocManager::install('rentrez')") | ||
| } | ||
| if (!requireNamespace("httr", quietly = TRUE) || | ||
| !requireNamespace("xml2", quietly = TRUE)) { | ||
| stop("Please install 'httr' and 'xml2' packages.") | ||
| } |
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similarly, if this is going to be an exported function we should source the required packages properly with @importFrom. Once the tags are added, running devtools::document() will populate the package NAMESPACE with the required package functions.
the-mayer
requested changes
Oct 29, 2025
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Great start! Everything works as described!
A couple of suggestions before approving/merging:
- Let's avoid using
library()andrequireNamespace()in user facing functions. Instead, we should rely on roxygen import tags to handle package dependencies. - MolEvolvR already has quite a few dependencies, it might be worth refactoring
acc2ipg()to usehttr2. That would let us drophttrand simplify the dependencies for the package
Thanks for putting this together and apologies for the delay in getting the review back to you!
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