larmanguide.Rmdphipcc in an R package designed to generate R Markdown reports for case-control studies of PhIP-seq data. phipcc builds analysis targets using the drake package from rOpenSci and Will Landau. phipcc also depends on phipmake, epitopefindr, and AVARDA.
This guide is written specifically for the Larman Lab and MARCC. Eventually I will write a more general guide.
There are two major phipcc functions that the user will interact with.
phipcc::define_plan_case_control() defines the computational case control plan to be executed by drake::make(). This function define_plan_case_control reads configuration settings from config.tsv, which will be discussed in depth in a later section of this guide.phipcc::render_from_template() reads in outputs from the case control plan and uses an R Markdown template to generate an HTML report. (the default template is provided in the package system.file("template_case_control.Rmd", package = "phipcc"), but custom templates can also be used.)Currently, define_plan_case_control() and the subsetquent call to drake::make() can be run on MARCC. However, the final step of knitting the final report depends on pandoc, a dependency that I haven’t yet figured out how to get working on MARCC. However, you can copy the necessary files to your local computer and run render_from_template locally.
cd /data/hlarman1/PhIPdb/Software/install_r_pkg
sbatch --export=pkg="brandonsie/drake" installGithub.sh
sbatch --export=pkg="brandonsie/phipmake" installGithub.sh
sbatch --export=pkg="brandonsie/phipcc" installGithub.sh
# Epitopefindr-specific setup
sbatch --export=pkg="brandonsie/epitopefindr" installGithub.sh
sbatch --export=pkg="mhahsler/rBLAST" installGithub.sh
sbatch --export=pkg="brandonsie/pdfuniter" installGithub.sh
sbatch --export=pkg="Biostrings" installBioc.sh
sbatch --export=pkg="IRanges" installBioc.sh
sbatch --export=pkg="msa" installBioc.sh
sbatch --export=pkg="S4Vectors" installBioc.sh
# Required (for steps that are not yet supported on MARCC)
if(!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("brandonsie/phipcc")
install.packages("pdftools")
# Optional (for steps that can be carried out either locally or on MARCC)
remotes::install_github("ropensci/drake")
remotes::install_github("brandonsie/phipmake")
remotes::install_github("brandonsie/epitopefindr")
remotes::install_github("mhahsler/rBLAST")
remotes::install_github("brandonsie/pdfuniter")
if (!requireNamespace("BiocManager")) install.packages("BiocManager")
BiocManager::install(c("Biostrings", "IRanges", "msa", "S4Vectors"))phipcc assumes that the phipmake pipeline including AVARDA has already been run on the data for your case and control samples.
A template is provided with field descriptions. In R, you can access this template by running file.copy(system.file("example_config.tsv", package = "phipcc"), "config.tsv"). For now, you will need to edit fields manually.
setwd("Local_Project_Directory") #Project Directory
phipcc::render_from_template(import_rdata = TRUE)