NEWS.md

In ropensci/rsnps: Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web

rsnps 0.6.0

MINOR IMPROVEMENTS

• 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)

BUG FIXES

• fix ncbi_snp_query(): fix so that it does not fail when rsid of SNP is no longer supported. (#157)

rsnps 0.5.0

NEW FEATURES

• ncbi_snp_query(): enable allele frequency for different reference populations, ncbi_snp_query() outputs now a tibble (#97).

MINOR IMPROVEMENTS

• 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.

DOCUMENTATION FIXES

• Updated vignette.

rsnps 0.4.0

MAJOR IMPROVEMENTS

NCBI / dbSNP changed their API:

• Rewrote ncbi_snp_query to accommodate the new API (#86, #88).
• Removed the functions ncbi_snp_query2 an ncbi_snp_summary.

MINOR IMPROVEMENTS

• Reordered ncbi_snp_query dataframe output to have chromosome and bp beside each other (#70).
• Changed ncbi_snp_query parameter (SNPs) to lower case (snps).

DOCUMENTATION FIXES

• Restructured and fixed a typo in README.Rmd and added link to vignette (#63).
• Added info of two new maintainers to DESCRIPTION.
• Added relevant API links to vignette.

BUG FIXES

• Fixed the test for allphenotypes function by making it less specific (#72).

rsnps 0.3.0

DEPRECATED AND DEFUNCT

• ld_search() is now defunct. The Broad Institute has taken down the SNAP service behind the function. (#46) (#53) (#60)

NEW FEATURES

• the three NCBI functions gain a new parameter 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)
• gains new function ncbi_snp_summary() for summary data on a SNP (#31)

MINOR IMPROVEMENTS

• http requests are now done using crul instead of httr (#44)
• now using markdown formatted documentation (#56)
• documented in ncbi_snp_query() that we can not change the assembly (#49)

BUG FIXES

• 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)

rsnps 0.2.0

NEW FEATURES

• 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)

MINOR IMPROVEMENTS

• Namespace all base R package function calls (#21)
• Improve httr::content call to parse to text, and encoding = "UTF-8" (#24)
• Added tests for ld_search() (#12)
• Added tests for ncbi_snp_query() and ncbi_snp_query2() (#13)
• Added ancestral allele output to ncbi_snp_query() (#23)

BUG FIXES

• Fix to fetch_genotypes(), was failing sometimes when the commented metadata lines at top varied in length (#22)
• Fix to ld_search() (#32)

rsnps 0.1.6

MINOR IMPROVEMENTS

• All examples now in \dontrun. (#11)
• Added additional tests for LDSearch() and NCBI_snp_query().
• Added a vignette.

BUG FIXES

• Bugs fixed in LDSearch(), which were actually bugs in NCBI_snp_query(). (#9)
• Bug fixed in NCBI_snp_query() as chromosome might also be "X".

rsnps 0.1.0

NEW FEATURES

• Bug fixes to all openSNP functions.

rsnps 0.0.5

NEW FEATURES

• released to CRAN

ropensci/rsnps documentation built on July 31, 2023, 11:11 a.m.