In jennasimit/flashfm: flexible and shared information fine-mapping

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Flashfm

The goal of flashfm is to use GWAS summary statistics to jointly fine-map genetic associations for several related quantitative traits in a Bayesian framework that leverages information between the traits.

Website available at: https://jennasimit.github.io/flashfm/.

Details available in https://rdcu.be/czYpf .

Hernandez, N., Soenksen, J., Newcombe, P., Sandhu, M., Barroso, I., Wallace, C., Asimit, J. The flashfm approach for fine-mapping multiple quantitative traits. Nat Commun 12, 6147 (2021). https://doi.org/10.1038/s41467-021-26364-y

System Requirements

Flashfm could be installed with ease on versions of R > 3.6.0. If installing on a Windows machine, Rtools must be installed. Installation time is estimated as 2 minutes.

Installation Guide

Short version

# install.packages("devtools")
devtools::install_github("jennasimit/flashfm")

Longer version (if above fails)

The following packages from CRAN and Bioconductor are required:

install.packages("Rcpp")
install.packages("RcppArmadillo")
install.packages("parallel")
install.packages("data.table")
install.packages("gtools")
install.packages("rlist")
install.packages("MASS")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("snpStats")

as well as the following dependencies from GitHUb

# install and load R2BGLiMS
remotes::install_github("pjnewcombe/R2BGLiMS")

NB: Must have a Java JDK installed in order to install and run R2BGLiMS. This is only needed if you need to run single-trait fine-mapping using JAM. If single-trait fine-mapping results are available, then it is not necessary to have Java JDK installed.

remotes::install_github("jennasimit/flashfm")
library(flashfm)
library(R2BGLiMS)  # if running internal JAM functions for single-trait fine-mapping

jennasimit/flashfm documentation built on July 31, 2022, 7:32 p.m.