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RápidoPGS 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.
2020-07-24 - First package version and attempt to submission to CRAN.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.