#' Hierarchical Interaction Score -- read results from matlab and write into R object
#'
#' @param project
#' @return nothing
#' @export
step_051_his <- function( project, nem_method, perturbed_genes, prepared_dir, nems_dir) {
matching <- dir(prepared_dir, pattern=project)
matching <- Filter(function(x) grepl(paste("\\.", "csv", sep=""), x), matching)
matching <- Filter(function(x) grepl(nem_method, x), matching)
for (input_file_name in matching) {
d <- read.csv(file.path(prepared_dir, input_file_name), header=FALSE)
rownames(d) <- perturbed_genes
colnames(d) <- perturbed_genes
l <- list()
l$graph <- d
output_file_name <- gsub("csv", "Rds", input_file_name)
saveRDS(l, file.path(nems_dir, output_file_name))
}
}
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