The genepi.utils package is a collection of utility functions for
working with genetic epidemiology data. For common use cases please see
the vignettes.
You can install the development version of genepi.utils like so:
# install.packages("devtools")
devtools::install_github("nicksunderland/genepi.utils")The package relies on the parallel processing capabilities of the
data.table,
furrr and
fst packages. These can be installed
like so:
install.packages("data.table")
install.packages("furrr")
install.packages("fst")Important: on mac it can be more challenging to enable OpenMP
parallel processing as the clang compiler does not include an OpenMP
runtime as standard. I recommend following the instructions on the
data.table GitHub
link. Key
for successful installation on my Macbook M2 Max was creating a Makevars
file in the root directory ~.R/Makevars, which is a simple text file,
containing the compilation flags below, and then re-installing from
source.
LDFLAGS += -L/opt/homebrew/opt/libomp/lib -lomp
CPPFLAGS += -I/opt/homebrew/opt/libomp/include -Xclang -fopenmpRe-install packages from source.
remove.packages("data.table")
remove.packages("furrr")
remove.packages("fstcore")
remove.packages("fst")
install.packages("https://cran.r-project.org/src/contrib/data.table_1.14.10.tar.gz", type="source", repos=NULL)
install.packages("https://cran.r-project.org/src/contrib/furrr_0.3.1.tar.gz", type="source", repos=NULL)
install.packages("https://cran.r-project.org/src/contrib/fstcore_0.9.18.tar.gz", type="source", repos=NULL)
install.packages("https://cran.r-project.org/src/contrib/fst_0.9.8.tar.gz", type="source", repos=NULL)For RSID mapping you will need a copy of the dbSNP .fst file
directory. Until this is hosted somewhere you will need to ask
nicholas.sunderland@bristol.ac.uk for the data files. If you are
working at the Bristol IEU the package should work on BC4. If not, ask
for the location of the dbSNP .fst file directory on the HPC. If you
use a custom location for the dbSNP directory you will need to set this
in the package - this only needs to be done once per package install.
set_dbsnp_directory("/path_to_directory/dbsnp")