Fixes a few variables and activates a forgotten conversion

VensinMa · Aug 5, 2020 · 210ecf2 · 210ecf2
1 parent 029be09
commit 210ecf2
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/pyRona/R/LFMM2_workflow.R b/pyRona/R/LFMM2_workflow.R
@@ -77,13 +77,14 @@ lfmm_estimates = function(env_file,
 
  env_file = env_file_compat(env_file)
 
- mod = lfmm2(input=genetic_data,
+ mod = lfmm2(input=geno_data,
  env=env_file,
  K=PCA_points)
 
  pv <- lfmm2.test(object=mod,
- input=genetic_data,
- env=env_file, linear = TRUE)
+ input=geno_data,
+ env=env_file,
+ linear = TRUE)
 
  pvalues <- t(pv$pvalues)
 
@@ -120,7 +121,7 @@ write_associations_table = function(assoc_table, pvalues){
 }
 
 ## Function invocation
-#convert_file(original_vcf, target_lfmm)
+convert_file(original_vcf, target_lfmm)
 genetic_data = read.lfmm(target_lfmm)
 
 PCA_points = preliminary_pca(genetic_data, PCA_points)