knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
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/.
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.
# install.packages("devtools") devtools::install_github("jennasimit/flashfm")
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
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.
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