Package: RapidoPGS 2.3.0.9001

RapidoPGS: A Fast and Light Package to Compute Polygenic Risk Scores

Quickly computes polygenic scores from GWAS summary statistics of either case-control or quantitative traits without parameter tuning. Reales,G., Vigorito, E., Kelemen,M., Wallace,C. (2021) <doi:10.1101/2020.07.24.220392> "RápidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset".

Authors:Guillermo Reales [aut, cre], Chris Wallace [aut], Olly Burren [ctb]

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RapidoPGS.pdf |RapidoPGS.html✨
RapidoPGS/json (API)
NEWS

# Install 'RapidoPGS' in R:

install.packages('RapidoPGS', repos = c('https://grealesm.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/grealesm/rapidopgs/issues

Datasets:

EUR_ld.blocks19 - LD block architecture for European populations (hg19).
EUR_ld.blocks38 - LD block architecture for European populations (hg38).
michailidou19 - Subset of Michailidou BRCA GWAS sumstat dataset.
michailidou38 - Subset of Michailidou BRCA GWAS sumstat dataset.

On CRAN:

5 exports 11 stars 1.71 score 94 dependencies 7 scripts 332 downloads

Last updated 14 days agofrom:05c9cd35c0. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 04 2024
R-4.5-win	NOTE	Sep 04 2024
R-4.5-linux	NOTE	Sep 04 2024
R-4.4-win	NOTE	Sep 04 2024
R-4.4-mac	NOTE	Sep 04 2024
R-4.3-win	NOTE	Sep 04 2024
R-4.3-mac	NOTE	Sep 04 2024

Exports:create_1000G gwascat.download rapidopgs_multi rapidopgs_single sd.prior.est

Dependencies:askpass BH bigassertr bigparallelr bigreadr bigsnpr bigsparser bigstatsr bigutilsr BiocGenerics bit bitops cli codetools coloc colorspace cowplot crayon curl data.table DEoptimR digest doParallel doRNG dplyr fansi farver ff flock foreach generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable httr IRanges irlba isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix matrixStats mgcv mime mixsqp munsell nabor nlme openssl parallelly pillar pkgconfig plyr ps R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl reshape RhpcBLASctl rlang rmio rngtools robustbase roptim RSpectra runonce S4Vectors scales susieR sys tibble tidyselect triebeard UCSC.utils urltools utf8 vctrs viridis viridisLite withr XVector zlibbioc

Computing a PGS using RápidoPGS-multi

Guillermo Reales

Rendered fromComputing_RapidoPGSmulti.Rmdusingknitr::rmarkdownon Sep 04 2024.

Last update: 2023-10-12
Started: 2021-04-14

Computing a PGS using RápidoPGS-single and GWAS catalog

Guillermo Reales

Rendered fromComputing_RapidoPGSsingle.Rmdusingknitr::rmarkdownon Sep 04 2024.

Last update: 2023-10-12
Started: 2021-04-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Download 1000 Genomes Phase III panel	create_1000G
LD block architecture for European populations (hg19).	EUR_ld.blocks19
LD block architecture for European populations (hg38).	EUR_ld.blocks38
Finding a file in an FTP directory This is an internal function to help 'gwascat.download' find the right file	find_file_in_ftp
Retrieve GWAS summary datasets from GWAS catalog ''gwascat.download' takes a PMID from the user and downloads the associated summary statistics datasets published in GWAS catalog	gwascat.download
Helper function to sum logs without loss of precision	logsum
Subset of Michailidou BRCA GWAS sumstat dataset.	michailidou19
Subset of Michailidou BRCA GWAS sumstat dataset.	michailidou38
Compute PGS from GWAS summary statistics using Bayesian sum of single-effect (SuSiE) linear regression using z scores	rapidopgs_multi
Compute PGS from GWAS summary statistics using posteriors from Wakefield's approximate Bayes Factors	rapidopgs_single
Compute Standard deviation prior (SD prior) for quantitative traits using pre-computed heritability.	sd.prior.est
Estimate trait variance, internal function	sdY.est
compute posterior probabilities using Wakefield's approximate Bayes Factors 'wakefield_pp' computes posterior probabilities for a given SNP to be causal for a given SNP under the assumption of a single causal variant.	wakefield_pp
Compute posterior probabilities using Wakefield's approximate Bayes Factors for quantitative traits	wakefield_pp_quant