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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

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Fine-mapping pipeline in R: FINEMAP, CAVIAR, PAINTOR, GCTA-COJO, ABF

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README

        

# finemapr

[![travis-ci build status](https://travis-ci.org/variani/finemapr.svg?branch=master)](https://travis-ci.org/variani/finemapr)

![](misc/figures/finemap-2causal.png)

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)