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RapidoPGS (development version)

RapidoPGS 2.3.1

RapidoPGS 2.3.1 2024-09-30

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

RapidoPGS 2.3.0

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

RapidoPGS 2.2.0.9000 2022-06-15

RapidoPGS 2.1.0

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

2020-08-03

  • 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.