stmgp-package {stmgp} | R Documentation |
Rapid and Accurate Genetic Prediction Modeling for Genome-Wide Association or Whole-Genome Sequencing Study Data
Description
Rapidly build accurate genetic prediction models for genome-wide association or whole-genome sequencing study data by smooth-threshold multivariate genetic prediction (STMGP) method. Variable selection is performed using marginal association test p-values with an optimal p-value cutoff selected by Cp-type criterion. Quantitative and binary traits are modeled respectively via linear and logistic regression models. A function that works through PLINK software (Purcell et al. 2007 <DOI:10.1086/519795>, Chang et al. 2015 <DOI:10.1186/s13742-015-0047-8>) <https://www.cog-genomics.org/plink2> is provided. Covariates can be included in regression model.
Details
The DESCRIPTION file: Index of help topics:
lapprox Compute lapprox stmgeplink Smooth-threshold multivariate genetic prediction (incorporating gene-environment interactions) for genome-wide association or whole-genome sequencing data in PLINK format stmgp Smooth-threshold multivariate genetic prediction stmgp-package Rapid and Accurate Genetic Prediction Modeling for Genome-Wide Association or Whole-Genome Sequencing Study Data stmgplink Smooth-threshold multivariate genetic prediction for genome-wide association or whole-genome sequencing data in PLINK format
Author(s)
Maintainer: Masao Ueki <uekimrsd@nifty.com>
References
Ueki M, Tamiya G, for Alzheimer's Disease Neuroimaging Initiative (2016) Smooth-thresholdmultivariate genetic prediction with unbiased model selection. Genet Epidemiol 40:233-43. <https://doi.org/10.1002/gepi.21958>
Ueki M (2009) A note on automatic variable selection using smooth-threshold estimating equations. Biometrika 96:1005-11. <https://doi.org/10.1093/biomet/asp060>
Ueki M, Fujii M, Tamiya G, for Alzheimer's Disease Neuroimaging Initiative and the Alzheimer's Disease Metabolomics Consortium (2019) Quick assessment for systematic test statistic inflation/deflation due to null model misspecifications in genome-wide environment interaction studies. PLoS ONE 14:e0219825. <https://doi.org/10.1371/journal.pone.0219825>
Ueki M, Tamiya G, for Alzheimer's Disease Neuroimaging Initiative (2021) mooth-threshold multivariate genetic prediction incorporating gene-nvironment interactions. G3 Genes|Genomes|Genetics 11:jkab278. <https://doi.org/10.1093/g3journal/jkab278>