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”.