NCBI / dbSNP changed their API:
ncbi_snp_query to accommodate the new API (#86, #88).ncbi_snp_query2 an ncbi_snp_summary.ncbi_snp_query dataframe output to have chromosome and bp beside each other (#70).ncbi_snp_query parameter (SNPs) to lower case (snps).README.Rmd and added link to vignette (#63).DESCRIPTION.allphenotypes function by making it less specific (#72).ld_search() is now defunct. The Broad Institute has taken down the SNAP service behind the function. (#46) (#53) (#60)key for passing in an NCBI Entrez API key. You can alternatively (and we encourage this) store your key as an environment variable and we’ll use that instead. The key allows you to have higher rate limits than without a key (#58)ncbi_snp_summary() for summary data on a SNP (#31)crul instead of httr (#44)ncbi_snp_query() that we can not change the assembly (#49)ncbi_snp_query2(): when many IDs passed in, we were failing with a “URI too long” message. We now check how many Ids are passed in and do a POST request as needed (#39)ncbi_snp_query() where it wasn’t pulling out correctly the gene name and BP position (#25)LDSearch() is now ld_search(), but LDSearch() still works until the next CRAN release when it will be defunct (#33)NCBI_snp_query() is now ncbi_snp_query(), but NCBI_snp_query() still works until the next CRAN release when it will be defunct (#33)NCBI_snp_query2() is now ncbi_snp_query2(), but NCBI_snp_query2() still works until the next CRAN release when it will be defunct (#33)httr::content call to parse to text, and encoding = "UTF-8" (#24)ld_search() (#12)ncbi_snp_query() and ncbi_snp_query2() (#13)ncbi_snp_query() (#23)fetch_genotypes(), was failing sometimes when the commented metadata lines at top varied in length (#22)ld_search() (#32)\dontrun. (#11)LDSearch() and NCBI_snp_query().LDSearch(), which were actually bugs in NCBI_snp_query(). (#9)NCBI_snp_query() as chromosome might also be “X”.