gwsem v0.1.5
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Genome-Wide Structural Equation Modeling
Melds genome-wide association tests with structural
equation modeling (SEM) using 'OpenMx'. This package contains low-level
C/C++ code to rapidly read genetic data encoded in U.K. Biobank or 'plink'
formats. Prebuilt modeling options include one and two factor
models. Alternately, analyses may utilize arbitrary, user-provided SEMs.
See Verhulst, Maes, & Neale (2017) <doi:10.1007/s10519-017-9842-6> for
details. An updated manuscript is in preparation.
Readme
gwsem
The goal of gwsem is to ...
Installation
You can install the released version of gwsem from CRAN with:
install.packages("gwsem")
Example
This is a basic example which shows you how to solve a common problem:
library(gwsem)
## basic example code
Functions in gwsem
| Name | Description | |
| buildOneItem | Build a model suitable for a single item genome-wide association study | |
| loadResults | Load GWAS results into a single data.frame | |
| setupThresholds | Set up thresholds for ordinal indicators | |
| gwsem-package | Genome-wide Structural Equation Modeling | |
| buildOneFac | Build a model suitable for a single factor genome-wide association study | |
| buildTwoFac | Build a model suitable for a two factor genome-wide association study | |
| prepareComputePlan | Return a suitable compute plan for a genome-wide association study | |
| GWAS | Run a genome-wide association study (GWAS) using the provided model | |
| buildOneFacRes | Build a model suitable for a single factor residual genome-wide association study | |
| setupCovariates | Set up model covariates | |
| No Results! | ||
Vignettes of gwsem
| Name | ||
| growth.Rmd | ||
| lgc-export.png | ||
| lgc-onyx.png | ||
| No Results! | ||
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Details
| Type | Package |
| License | GPL (>= 3) |
| Encoding | UTF-8 |
| LazyData | true |
| Language | en-US |
| LinkingTo | BH (>= 1.69.0-1) |
| RoxygenNote | 6.1.1 |
| SystemRequirements | GNU make |
| URL | https://github.com/jpritikin/gwsem |
| BugReports | https://github.com/jpritikin/gwsem/issues |
| NeedsCompilation | yes |
| VignetteBuilder | knitr |
| Packaged | 2019-10-15 16:59:24 UTC; joshua |
| Repository | CRAN |
| Date/Publication | 2019-10-15 22:10:06 UTC |
| linkingto | BH (>= 1.69.0-1) |
| suggests | covr , knitr , MASS , qqman , rmarkdown , testthat (>= 2.1.0) |
| imports | data.table , methods |
| depends | OpenMx (>= 2.14) , R (>= 3.5) |
| Contributors | Yann Collet, Facebook, Inc. , Bradley Verhulst, Gavin Band, Yuta Mori, Shaun Purcell, Christopher Chang, Wojciech Mula, Kim Walisch |
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