diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/computations/biweight.R | 19 | ||||
| -rw-r--r-- | gn3/computations/biweight.py | 8 |
2 files changed, 22 insertions, 5 deletions
diff --git a/gn3/computations/biweight.R b/gn3/computations/biweight.R index 05f7145..650c5fd 100644 --- a/gn3/computations/biweight.R +++ b/gn3/computations/biweight.R @@ -1,5 +1,5 @@ -library(WGCNA) +# library(WGCNA) myArgs <- commandArgs(trailingOnly = TRUE) @@ -7,9 +7,22 @@ trait_vals <- as.numeric(unlist(strsplit(myArgs[1], split=" "))) target_vals <- as.numeric(unlist(strsplit(myArgs[2], split=" "))) BiweightMidCorrelation <- function(trait_val,target_val){ - results <- bicorAndPvalue(x,y) + results <- bicorAndPvalue(trait_val,target_val) return (list(c(results$bicor)[1],c(results$p)[1])) } -cat(BiweightMidCorrelation(trait_vals,target_vals)) + + + + +# the idea is that you get the entire dataset in any format +# and then do ther correlation + +ComputeAll <-function(trait_val,target_dataset) { + for target_val in target_dataset { + results = BiweightMidCorrelation(trait_val,target_val) + cat(BiweightMidCorrelation(trait_vals,target_vals)) + } +} + diff --git a/gn3/computations/biweight.py b/gn3/computations/biweight.py index c17de8e..e598a5b 100644 --- a/gn3/computations/biweight.py +++ b/gn3/computations/biweight.py @@ -2,17 +2,21 @@ """module contains script to call biweight mid\ correlation in R""" - import subprocess +import os +from pathlib import Path from typing import List +FILE_PATH = os.path.join(Path(__file__).parent.absolute(), "biweight.R") + def call_biweight_script(trait_vals: List, target_vals: List, - path_to_script: str = "./biweight_R", + path_to_script: str = FILE_PATH, command: str = "Rscript" ): '''biweight function''' + args_1 = ' '.join(str(trait_val) for trait_val in trait_vals) args_2 = ' '.join(str(target_val) for target_val in target_vals) cmd = [command, path_to_script] + [args_1] + [args_2] |