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https://github.com/variani/finemapr
Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF
https://github.com/variani/finemapr
caviar fine-mapping finemap paintor rpackage rstats
Last synced: 3 months ago
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Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF
- Host: GitHub
- URL: https://github.com/variani/finemapr
- Owner: variani
- License: gpl-3.0
- Created: 2018-02-09T17:19:05.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2024-01-16T19:57:52.000Z (10 months ago)
- Last Synced: 2024-06-05T02:32:40.374Z (5 months ago)
- Topics: caviar, fine-mapping, finemap, paintor, rpackage, rstats
- Language: R
- Homepage:
- Size: 1.2 MB
- Stars: 27
- Watchers: 2
- Forks: 12
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- jimsghstars - variani/finemapr - Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF (R)
README
# finemapr
[](https://travis-ci.org/variani/finemapr)
R interface to fine-mappers:
- FINEMAP http://www.christianbenner.com/
- CAVIAR https://github.com/fhormoz/caviar
- PAINTOR https://github.com/gkichaev/PAINTOR_V3.0
By using `finemapr`, your input files are automatically prepared for each tool, the analysis workflow is tool-independent; and exploration of fine-mapping results is powered by R in printing/plotting/data export.
**Note**: the package is still under development and its current version is not stable. The current work aims at switching from `run_` functions to a more general one, [finemapr](https://github.com/variani/finemapr/blob/master/R/finemapr.R). The later function makes use of S3 method dispatch features. Thus, use this package with caution until the stable release comes out.
## Quick start
```r
library(finemapr)
library(tidyverse)
# get some example data
finemapr::example_finemap() %>% attach
# run finemapping, default tool is finemap
out <- finemapr(z1, ld1, n1, args = "--n-causal-max 3")
# print & plot results
out
plot(out, grid_nrow = 1)
```
## Tool-independent analysis workflow
```r
# set up
options(finemapr_ = "")
# read input files
my_zscores <- read_zscores("")
my_ld <- read_ld("")
# run analysis
# depreciated, but still works: out <- run_(my_zscores, my_ld, args = "")
out <- finemapr(my_zscores, my_ld, method = "", args = "")
# explore results
print(out)
head(out$snp) # main table of results
plot(out)
# export results
write.table(out$snp, "")
```
## Examples
See the vignette [Fine-mapping analysis pipeline by `finemapr`](https://variani.github.io/finemapr/vignettes/finemapr.html).
## Related projects
- [FineMapping pipeline using GWAS summary statistics](https://github.com/jinghuazhao/FM-pipeline)
- [Finemapping pipeline that automates the usage of PAINTOR, and CAVIAR BF](https://github.com/theboocock/fine_mapping_pipeline)