NEWS

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RapidoPGS 2.3.2 (2026-04-03)

RapidoPGS 2.3.2 2026-03-30

• Fixed issues with GenomeInfoDb that caused RapidoPGS to be archived on CRAN.

RapidoPGS 2.3.1 (2025-02-19)

RapidoPGS 2.3.1 2024-09-30

• Replace type by trait within rapidopgs_multi() to match the parameter call.

RapidoPGS 2.3.0 (2023-10-13)

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 (2022-06-15)

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 (2021-06-17)

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

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.

RapidoPGS 1.0.2 (2020-08-07)

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.

RapidoPGS 1.0.1

2020-07-24

• First package version and attempt to submission to CRAN.