pecotmr

This R package, pecotmr implements pair-wise enrichment, colocalization, TWAS and Mendelian Randomization to integrate QTL and GWAS analysis based on fine-mapped single effects model. pecotmr also stands for a probabilistic ecosystem consolidating a range of established and new models into a streamlined, user-friendly interface complete with well-documented examples that will help getting your analysis done by tomorrow if you start working on it today!

This project was developed by NIH/NIA FunGen-xQTL Project Working Group members with applications to FunGen-xQTL data analysis.

Quick Start

To install the latest version of the pecotmr package from GitHub, use BiocManager:

install.packages(c("BiocManager", "remotes"))
BiocManager::install("cumc/pecotmr")

If you have cloned the repository locally, you can install the package with the install_local function from devtools. Assuming your working directory contains the pecotmr repository, run this code to install the package:

devtools::install_local("pecotmr",build_vignettes = TRUE)

devtools should automatically install all required packages if they are not installed already. If automatic installation fails for some packages and you are unable to fix them, please try to use our conda package instead.

To install using conda or micromamba for our released version,

micromamba install -c dnachun -c conda-forge -c bioconda r-pecotmr

To still use devtools to build pecotmr from source we suggest you build a local conda environment for pecotmr and all its dependencies,

cp .github/environment/environment.yaml /tmp/environment.yaml
grep -v '{%' < .github/recipe/meta.yaml | yq .requirements.host | sed 's/^/  /' >> /tmp/environment.yaml
micromamba create -f /tmp/environment.yaml

then use

micromamba activate pecotmr

to activate it. Now you should be able to build pecotmr from source.

Developer's notes

• When any changes are made to roxygen2 markup or the C++ code in the src directory, run devtools::document() to update the RcppExports.cpp, the package namespaces (see NAMESPACE), and the package documentation files (in the "man" subdirectory),

• These are the R commands to build the website (make sure you are connected to Internet while running these commands):

  pkgdown::build_site(lazy=TRUE, examples=FALSE)

• To format R codes in the R folder,

  for i in `ls R/*.R`; do bash inst/misc/format_r_code.sh $i; done

• After editing C++ code in the src directory, please use uncrustify (version >=0.74.0, available from conda-forge) to format the code using configuration file inst/misc/uncrustify_default.cfg. For example:

  uncrustify -c inst/misc/uncrustify_default.cfg --replace --no-backup -l CPP src/qtl_enrichment.cpp
  uncrustify -c inst/misc/uncrustify_default.cfg --replace --no-backup -l CPP src/qtl_enrichment.hpp

• Prior to submitting the package to Bioconductor, the following modifications need to be made: (1) remove the Remotes: entry in DESCRIPTION; and (2) remove the fastenloc.Rmd vignette.