Merge pull request #20 from genenetwork/feature/biweight-correlation

add biweight r script and tests

1 files changed, 42 insertions, 0 deletions

diff --git a/scripts/calculate_biweight.R b/scripts/calculate_biweight.R
new file mode 100644
index 0000000..bad93cb
--- /dev/null
+++ b/scripts/calculate_biweight.R
@@ -0,0 +1,42 @@
+
+library(testthat)
+library(WGCNA)
+
+arg_values <- commandArgs(trailingOnly = TRUE)
+ParseArgs <- function(args){
+
+    trait_vals <- as.numeric(unlist(strsplit(args[1], split=" ")))
+    target_vals <- as.numeric(unlist(strsplit(args[2], split=" ")))
+
+    return(list(trait_vals= c(trait_vals),target_vals = c(target_vals)))
+
+}
+BiweightMidCorrelation <- function(trait_val,target_val){
+
+    results <- bicorAndPvalue(c(trait_val),c(target_val))
+    return ((c(c(results$bicor)[1],c(results$p)[1])))
+
+}
+
+
+
+test_that("biweight results"),{
+    vec_1 <- c(1,2,3,4)
+    vec_2 <- c(1,2,3,4)
+
+    results <- BiweightMidCorrelation(vec_1,vec_2)
+    expect_equal(c(1.0,0.0),results)
+}
+
+
+test_that("parsing args "),{
+    my_args <- c("1 2 3 4","5 6 7 8")
+    results <- ParseArgs(my_args)
+
+    expect_equal(results[1],c(1,2,3,4))
+    expect_equal(results[2],c(5,6,7,8))
+}
+
+parsed_values <- ParseArgs(arg_values)
+
+cat((BiweightMidCorrelation(parsed_values[1],parsed_values[2])))
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