README.md

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/.

System Requirements

Flashfm could be installed with ease on versions of R > 3.6.0 and requires additional steps for 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")
install.packages("xtable")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("snpStats")
BiocManager::install("mixOmics")     

as well as the following dependencies from GitHUb

install.packages("remotes")
# install and load GUESSFM
remotes::install_github("chr1swallace/GUESSFM","nor2guess")
# install and load MFM
remotes::install_github("jennasimit/MFM")
# 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
NOTE: If R < 3.5.1, to install mixOmics do the following:

Go to https://cran.r-project.org/src/contrib/Archive/mixOmics/ and download mixOmics_6.3.2.tar.gz. Then, in R:

install.packages("mixOmics", repos = "mixOmics_6.3.2.tar.gz", type="source")

where if in a different working directory than where the zip file is contained, a file path may be needed for the repos argument.



jennasimit/flashfm documentation built on Aug. 9, 2021, 7:36 a.m.