In variani/finemapr: R wrapper to fine-mappers

opts_chunk$set(dev = "png", dev.args = list(type = "cairo"), dpi = 192, fig.path = "figures/", comment = NA, results = 'markup', tidy = F, message = F, warning = F, echo = T)

library(devtools)
load_all("~/git/variani/finemapr")

# specify where the FINEMAP tool is located (user-specific)
# - the user needs to download and install the tool before the analysis
# - here, the tool binary file is stored in `~/apps/finemap/` directory
options(finemapr_finemap = "~/apps/finemap/finemap")

# load example data from FINEMAP (http://www.christianbenner.com/)
# - data are obtained from the same directory `~/apps/finemap/`, subdirectory `example`
ex <- example_finemap()

# run the tool
# - simulated data in region 1 (used here in the analysis) assumed 2 causal SNPs
# - arg. #1: table with SNP name and Z-score in the first 2 columns
# - arg. #2: the LD matrix with colnames/rownames corresponding to SNP names
# - arg. #3: the number of invidivudals
# - arg. `args`: pass other arguments to the tool as a string 
out <- run_finemap(ex$tab1, ex$ld1, ex$n1, args = "--n-causal-max 3")

print(out)

plot(out, label_size = 3, grid_ncol = 1)

variani/finemapr documentation built on Dec. 12, 2020, 9:40 p.m.