- allgensnp(): previously the dataframe returned contained duplicate "name" columns. Now the "name" column that contains the submitter's name has been renamed "user_name" and the snp rsid name remains "name". (#67)
- allgensnp(): added a parameter "usersubset" which allows to download a subset of users for the particular rsid. (#167)
- improved test coverage from 71 to 76% making use of {vcr} with some test fixtures.
- some typos and formatting improved (#167)
- fix ncbi_snp_query(): fix so that it does not fail when rsid of SNP is no longer supported. (#157)
- ncbi_snp_query(): enable allele frequency for different reference populations, ncbi_snp_query() outputs now a tibble (#97).
- ncbi_snp_query(): replace calls to RJSONIO with equivalent in jsonlite (#98).
- unit tests for ncbi_snp_query(): added a tolerance to any allele frequency checks.
- move vignette source to /vignettes and precompute using an R script.
- Updated vignette.
NCBI / dbSNP changed their API:
- Rewrote
ncbi_snp_queryto accommodate the new API (#86, #88). - Removed the functions
ncbi_snp_query2anncbi_snp_summary.
- Reordered
ncbi_snp_querydataframe output to have chromosome and bp beside each other (#70). - Changed
ncbi_snp_queryparameter (SNPs) to lower case (snps).
- Restructured and fixed a typo in
README.Rmdand added link to vignette (#63). - Added info of two new maintainers to
DESCRIPTION. - Added relevant API links to vignette.
- Fixed the test for
allphenotypesfunction 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)
- the three NCBI functions gain a new parameter
keyfor 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) - gains new function
ncbi_snp_summary()for summary data on a SNP (#31)
- http requests are now done using
crulinstead ofhttr(#44) - now using markdown formatted documentation (#56)
- documented in
ncbi_snp_query()that we can not change the assembly (#49)
- fix to
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) - fixed problem in
ncbi_snp_query()where it wasn't pulling out correctly the gene name and BP position (#25)
LDSearch()is nowld_search(), butLDSearch()still works until the next CRAN release when it will be defunct (#33)NCBI_snp_query()is nowncbi_snp_query(), butNCBI_snp_query()still works until the next CRAN release when it will be defunct (#33)NCBI_snp_query2()is nowncbi_snp_query2(), butNCBI_snp_query2()still works until the next CRAN release when it will be defunct (#33)
- Namespace all base R package function calls (#21)
- Improve
httr::contentcall to parse to text, andencoding = "UTF-8"(#24) - Added tests for
ld_search()(#12) - Added tests for
ncbi_snp_query()andncbi_snp_query2()(#13) - Added ancestral allele output to
ncbi_snp_query()(#23)
- Fix to
fetch_genotypes(), was failing sometimes when the commented metadata lines at top varied in length (#22) - Fix to
ld_search()(#32)
- All examples now in
\dontrun. (#11) - Added additional tests for
LDSearch()andNCBI_snp_query(). - Added a vignette.
- Bugs fixed in
LDSearch(), which were actually bugs inNCBI_snp_query(). (#9) - Bug fixed in
NCBI_snp_query()as chromosome might also be "X".
- Bug fixes to all openSNP functions.
- released to CRAN