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RápidoPGS: a rapid polygenic score calculator for summary GWAS data without a test dataset
- Source :
- Bioinformatics
- Publication Year :
- 2021
- Publisher :
- Oxford University Press (OUP), 2021.
-
Abstract
- Motivation Polygenic scores (PGS) aim to genetically predict complex traits at an individual level. PGS are typically trained on genome-wide association summary statistics and require an independent test dataset to tune parameters. More recent methods allow parameters to be tuned on the training data, removing the need for independent test data, but approaches are computationally intensive. Based on fine-mapping principles, we present RápidoPGS, a flexible and fast method to compute PGS requiring summary-level Genome-wide association studies (GWAS) datasets only, with little computational requirements and no test data required for parameter tuning. Results We show that RápidoPGS performs slightly less well than two out of three other widely used PGS methods (LDpred2, PRScs and SBayesR) for case–control datasets, with median r2 difference: -0.0092, -0.0042 and 0.0064, respectively, but up to 17 000-fold faster with reduced computational requirements. RápidoPGS is implemented in R and can work with user-supplied summary statistics or download them from the GWAS catalog. Availability and implementation Our method is available with a GPL license as an R package from CRAN and GitHub. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects :
- Statistics and Probability
Multifactorial Inheritance
AcademicSubjects/SCI01060
Genotype
Computer science
Gwas data
Posterior probability
Genome-wide association study
Machine learning
computer.software_genre
Polymorphism, Single Nucleotide
Biochemistry
law.invention
Set (abstract data type)
03 medical and health sciences
0302 clinical medicine
law
Range (statistics)
Molecular Biology
030304 developmental biology
Supplementary data
0303 health sciences
Training set
business.industry
Genetics and Population Analysis
Function (mathematics)
Individual level
Original Papers
Computer Science Applications
Test (assessment)
Computational Mathematics
R package
Computational Theory and Mathematics
Calculator
Data mining
Artificial intelligence
business
computer
030217 neurology & neurosurgery
Genome-Wide Association Study
Test data
Subjects
Details
- ISSN :
- 14602059 and 13674803
- Volume :
- 37
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....4ad312ed9b33211863cda45bc9abcc8d