https://github.com/nanxstats/cats
Joint power analysis for non-symmetric two-stage case-control designs
https://github.com/nanxstats/cats
clinical-trials gwas power-analysis sample-size-calculation
Last synced: 3 months ago
JSON representation
Joint power analysis for non-symmetric two-stage case-control designs
- Host: GitHub
- URL: https://github.com/nanxstats/cats
- Owner: nanxstats
- License: gpl-3.0
- Created: 2019-05-11T03:39:45.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2021-12-21T05:40:06.000Z (almost 4 years ago)
- Last Synced: 2025-03-05T22:11:50.662Z (7 months ago)
- Topics: clinical-trials, gwas, power-analysis, sample-size-calculation
- Language: CSS
- Homepage: https://nanx.me/cats/
- Size: 2.06 MB
- Stars: 2
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# cats
[](https://github.com/nanxstats/cats/actions)
`cats` is a fork of the R package `CATS` developed by Anders Albrechtsen <> for power estimation in two-stage genome-wide association designs. See [the vignette](https://nanx.me/cats/articles/cats.html) for code examples.
## Installation
```r
# install.packages("devtools")
devtools::install_github("nanxstats/cats")
```
## Method
The method for power analysis implemented in `CATS` is based on Skol et al. 2006, but more generalized so that the ratio between cases and controls may vary between stages. The allele frequencies, disease prevalence, and relative risk can also vary.
## Changes
The changes made to the original R package `CATS` are only for fixing the package build and check issues (under R 3.6.0 as of May 2019), for example:
- Used unified lowercase names for package and functions
- Fixed C code build errors and warnings (now passes clang)
- Fixed other package formatting issues that blocks building and checking
- Used roxygen2 to automate namespace and documentation generation
- Organized the existing code examples as a vignette
## Source
This package is forked and modified from these resources. They are also available as archives under `bin/`:
- [Code examples](http://www.popgen.dk/software/index.php/CATS)
- [Source tarball](http://popgen.dk/software/download/CATS/CATS_1.02.tar.gz)
- [PDF manual](http://popgen.dk/software/download/CATS/CATS-manual.pdf)
## References
- Skol AD, Scott LJ, Abecasis GR, Boehnke M: Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 38: 209-213, 2006.