#' Correlation between s-genes
#'
#' @param project
#' @return nothing
#' @export
step_052_correlation <- function( project, perturbed_genes, prepared_dir, nems_dir) {
#from prepared data, find egenes == sgenes
matching <- dir(prepared_dir, pattern=project)
matching <- Filter(function(x) grepl(paste("\\.", "Rds", sep=""), x), matching)
for (input_file_name in matching) {
expr_data <- readRDS(file.path(prepared_dir, input_file_name))
x <- expr_data[perturbed_genes, perturbed_genes]
net <- cor(x)
net[net<0] <- 0 # negative correlation isn't interesting
# put object in nem format
l <- list()
l$graph <- net
output_file_name <- paste("cor", input_file_name, sep=".")
saveRDS(l, file.path(nems_dir, output_file_name))
}
}
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