R package for simultaneous fine-mapping of genetic associations for several diseases, in a Bayesian framework that borrows information between the diseases.
Website available at: https://jennasimit.github.io/MFM/.
MFMextra has simulation code for evaluating MFM and is available at: https://jennasimit.github.io/MFMextra/. A MFM demo is available in the vignettes of MFM. In our tests in ran in under 5 seconds.
MFM could be installed with ease on versions of R > 3.5 and requires additional steps for R < 3.5. Installation has been tested on R 3.5.1. Installation time is estimated as 2 minutes.
MFM is purely an R package and so is platform independent. It depends on the R package GUESSFM, which depends on the software GUESS, available at http://www.bgx.org.uk/software/guess.html, but can be more easily installed via the R package R2GUESS, which is a dependency of GUESSFM. GUESSFM is described in the paper http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005272 and GUESS is described in the paper http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003657.
To install, you may first need some R package dependencies, the packages snpStats, GUESSFM, BMA, Rcpp, RcpArmadillo, parallel, data.table, gtools, fields, cowplot, dplyr. E.g., if you don’t have some of these packages, from inside R, do
install.packages("BMA") install.packages("Rcpp") install.packages("RcppArmadillo") install.packages("parallel") install.packages("data.table") install.packages("gtools") install.packages("fields") install.packages("cowplot") unstall.packages("dplyr")
Some packages (e.g. snpStats) are from Bioconductor. For these, you need to do
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("snpStats")
R2GUESS, a dependency of GUESSFM, has the dependency mixOmics, which is available from Bioconductor for R versions >=3.5 and at cran in archive form for R < 3.5.
# R >= 3.5: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("mixOmics")
R < 3.5:
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.
GUESSFM is from github and to install do
install.packages("devtools") # if you don't already have the package library(devtools) install_github("chr1swallace/GUESSFM")
Then, to install MFM, also from github, do
install.packages("devtools") # if you don't already have the package library(devtools) install_github("jennasimit/MFM")
Run the following to generate the MFM website:
Rscript -e "pkgdown::build_site()"