#' tardbpdms_epistasis_analysis
#'
#' Epistasis analysis.
#'
#' @param toxicity_path path to R data object with single and double mutant toxicity values (required)
#' @param miscpath path to misc scripts and data directory (required)
#' @param DMS2structure_path Path to DMS2structure repository (required)
#' @param numCores Number of available CPU cores (default:1)
#' @param execute whether or not to execute the analysis (default: TRUE)
#'
#' @return Nothing
#' @export
#' @import data.table
tardbpdms_epistasis_analysis <- function(
toxicity_path,
miscpath,
DMS2structure_path,
numCores = 1,
execute = TRUE
){
#Do nothing if analysis not executed
if(!execute){
return()
}
#Display status
message(paste("\n\n*******", "running stage: tardbpdms_epistasis_analysis (this might take a while; you may want to adjust 'numCores' argument, DEFAULT=10)", "*******\n\n"))
#Create output directory
tardbpdms__create_dir(tardbpdms_dir = file.path(miscpath, "misc_epistasis_analysis"))
### Run misc script on command-line
###########################
system(paste0(
file.path(miscpath, "scripts", "tardbpdms__epistasis_analysis.R"),
" -i ",
toxicity_path,
" -o ",
file.path(miscpath, "misc_epistasis_analysis"),
" -d ",
DMS2structure_path,
" -c ",
numCores))
}
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