update naming

geneAccord_AML.R

@@ -5,31 +5,27 @@ library(tidyr)
 
 # test if GeneAccord is installed
 GeneAccordFlag <- FALSE
-try(GeneAccordFlag <- packageVersion("GeneAccord") > '1.0.0', silent = TRUE)
+#try(GeneAccordFlag <- packageVersion("GeneAccord") > '1.0.0', silent = TRUE)
 
 if(GeneAccordFlag) {
   library(GeneAccord)
 } else {
   source("./R/geneAccord_fns.R")
 }
 
-
 # read in data
 clone_df <- read.table("./data/AMLsubclones_trees.txt", header = TRUE)
 # process clone data frame into clonal exclusivity data frame
 cx_df <- clone_df_to_cx_df(clone_df)
 # select only gene pairs in more than 4 patients
 cx_selected <- filter_cx_df(cx_df, 4)
 
-# run the standard geneAccord testing
-cx_results <- geneAccord(cx_selected)
-cx_results
+# run the placement geneAccord testing
+(place_results <- geneAccord(cx_selected))
 
-# run testing of patient selection
-pat_results <- geneAccord(cx_selected, test_type = "patient")
-pat_results
+# run occurrence geneAccord testing
+(occur_results <- geneAccord(cx_selected, test_type = "occurrence"))
 
-# run combined testing of patient selection and 
+# run combined testing of occurrence in patients and 
 # location of gene pairs in those patients
-comb_results <- geneAccord(cx_selected, test_type = "combined")
-comb_results
+(comb_results <- geneAccord(cx_selected, test_type = "combined"))