NEWS.md
RapidoPGS 2.3.0.9002 2024-09-30 - Replace type by trait within rapidopgs_multi() to match the parameter call.
RapidoPGS 2.3.0.9001 2024-09-04 - Fixed a bug derived from check_dataset() in runsusie() requiring sdY for quantitative traits in rapidopgs_multi(). SuSiE doesn’t require it so we know detect if type = "quant" and pass sdY = 1 onto runsusie().
RapidoPGS 2.3.0 2023-10-12 - We updated rapidopgs_multi() to accommodate updates in both coloc and susieR. This involved adding some arguments (N, sample size), and removing others (pi_i, prior probability, now automatically computed by SuSiE). We also now allow the user to supply their own LD block file for non-European GWAS. - Fixed gwascat.download() to accommodate the new GWAS catalog file structure. Now it is more interactive, providing extra flexibility. - Updated vignettes. - Updated hg38 LD blocks file from its original repository, which was also updated.
RapidoPGS 2.2.0.9000 2022-06-15 - We updated hg38 LD blocks from liftovered Berisa & Pickrell to recomputed MacDonald et al. 2022 (https://github.com/jmacdon/LDblocks_GRCh38, https://www.biorxiv.org/content/10.1101/2022.03.04.483057v1), which offer a more accurate representation of LD structure in hg38.
RapidoPGS 2.1.0.9009 2021-09-28 - Fixed a bug derived from automatically supplying “nref” to SuSIE in rapidopgs_multi(), which is no longer required.
RapidoPGS 2.1.0.9008 2021-08-13 - Fixed a change in the hard-coded url to download 1000G panel from the official server to meet a change in versioning (v5a -> v5b) at the source.
RapidoPGS 2.1.0.9007 2021-07-13 - Fixed a bug caused by changes in behavior of runsusie() in rapidopgs_multi() that used to supply an extra zero element which is not supplied anymore.
RapidoPGS 2.1.0.9006 2021-07-12 - Fixed an error popping up when rapidopgs_multi() is not supplied input of data.table class. - Removed a deprecated argument in runsusie() internal function that was preventing rapidopgs_multi() to run properly.
RapidoPGS 2.1.0.9005 2021-07-09 - Fixed a change in the hard-coded url to download 1000G panel from the official server to meet a change in versioning for sex chromosomes at the source.
RapidoPGS 2.1.0.9004 2021-06-17 - Tiny updates in README and vignettes concerning dependencies and versions.
RapidoPGS 2.1.0.9003 2021-06-09 - Removed need for N_LD in rapidopgs_multi().
RapidoPGS 2.1.0.9002 2021-06-08 - Updated dependency versions. - Change some stuff for CRAN submission.
RapidoPGS 2.1.0.9001 2021-04-14 - New vignette for rapidopgs_multi() and minor changes in rapidopgs_single() vignette. - New dataset michailidou19, analogous to michailidou but in hg19 build, required for rapidopgs_multi() examples.
2021-03-08 - New implementation of rapidopgs_multi(), which now allows to use pre-computed LD matrices. - rapidopgs_multi() now uses a different susie implementation, as implemented in coloc package. - rapidopgs_multi() added parameters to select trait type, as well as path to LD matrices, and sample size for the dataset used for LD matrix computation. - coloc added as a dependency.
RapidoPGS 2.0.0.9001 2021-01-27 - Fixed bug in rapidopgs_single() that prevented it for running for quantitative traits. - Fixed missing space in message for users in rapidopgs_single().
2020-12-17 - Changed function name computePGS() to rapidopgs_single(). - rapidopgs_single() dropped the requirement for MAF for case-control traits. - rapidopgs-single() added a parameter to select type of trait (case-control or quantitative) of the dataset used in the call. - rapidopgs_multi() function added, which applies SuSiE method to PGS computing. - susieR added as a dependency. - create_1000G() added, which automatically download and sets up a reference panel for rapidopgs_multi() from 1000 Genomes Phase III. - sd.prior.est() function added to use heritability estimates to create an informed SD prior.
2020-08-03 - Corrected description paragraph to not mention the package itself. Now it starts as “Quickly computes…”. - Included package reference (authors (year), <doi:…>) in DESCRIPTION. - Olly Burren added as a contributor - Included reference to preprint in README. - Included executable examples in the exported functions. - Updated the website to include links to GitHub on the side.