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_<tool> functions to a more general one, finemapr. The later function makes use of S3 method dispatch features. Thus, use this package with caution until the stable release comes out.
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)# set up
options(finemapr_<tool> = "<path to fine-mapping tool>")
# read input files
my_zscores <- read_zscores("<my_scores.tab>")
my_ld <- read_ld("<my_ld.tab>")
# run analysis
# depreciated, but still works: out <- run_<tool>(my_zscores, my_ld, args = "<custom arguments>")
out <- finemapr(my_zscores, my_ld, method = "<tool>", args = "<custom arguments>")
# explore results
print(out)
head(out$snp) # main table of results
plot(out)
# export results
write.table(out$snp, "<my_results.tab>")See the vignette Fine-mapping analysis pipeline by finemapr.