changing params.is_binary to accomadate continuous outcome.

Author: davidenoma

scripts/skat.R

@@ -181,6 +181,7 @@ genotype_path <- args[4]
 weights_type <- args[5]
 chr <- args[6]
 is_binary <- ifelse(length(args) > 6, as.logical(args[7]), TRUE)
+chr <- gsub("chr", "", chr)
 
 result_folder <- "result_folder"
 prepare_SKAT_files_per_chr(genotype_path, genotype_prefix)

scripts/skat_unweighted.R

@@ -176,6 +176,10 @@ chr <- args[4]
 output_folder <- args[5]
 is_binary <- ifelse(length(args) > 5, as.logical(args[6]), TRUE)
 
+chr <- gsub("chr", "", chr)
+#work on code for result folder
+result_folder <- output_folder
+
 # Perform SKAT analysis for the given chromosome
 prepare_SKAT_files_per_chr(genotype_path, genotype_prefix)
 print("Done creating SKAT genotype")