NEWS

RapidoPGS 2.3.0.9002

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

RapidoPGS 2.1.0.9003 2021-06-09

RapidoPGS 2.1.0.9002 2021-06-08

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.

2020-07-24