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), ) 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.
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