Commented out debug code. (#66)

Author: jamesnemesh

R/bican.mccarroll.figures/R/de_eqtl_filtering_plots.R

@@ -6,18 +6,18 @@
 ## Set configuration (development only; comment out in package build)
 ## ------------------------------------------------------------------
 
-source("R/paths.R")
-
-options(
-    bican.mccarroll.figures.data_root_dir =
-        "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis",
-
-    bican.mccarroll.figures.out_dir =
-        "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis/figure_repository",
-
-    bican.mccarroll.figures.cache_dir =
-        "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis/figure_repository/data_cache"
-)
+# source("R/paths.R")
+#
+# options(
+#     bican.mccarroll.figures.data_root_dir =
+#         "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis",
+#
+#     bican.mccarroll.figures.out_dir =
+#         "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis/figure_repository",
+#
+#     bican.mccarroll.figures.cache_dir =
+#         "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis/figure_repository/data_cache"
+# )
 
 
 #########################################

R/bican.mccarroll.figures/R/volanco_plots.R

@@ -1,17 +1,17 @@
-source("R/paths.R")
-
-options(
-    bican.mccarroll.figures.data_root_dir =
-        "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis",
-
-    bican.mccarroll.figures.out_dir =
-        "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis/figure_repository",
-
-    bican.mccarroll.figures.cache_dir =
-        "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis/figure_repository/data_cache"
-)
-
-de_dir<-gene_to_chr_file<-ct_file<-outDir<-data_cache_dir<- NULL
+# source("R/paths.R")
+#
+# options(
+#     bican.mccarroll.figures.data_root_dir =
+#         "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis",
+#
+#     bican.mccarroll.figures.out_dir =
+#         "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis/figure_repository",
+#
+#     bican.mccarroll.figures.cache_dir =
+#         "/broad/bican_um1_mccarroll/RNAseq/analysis/CAP_freeze_3_analysis/figure_repository/data_cache"
+# )
+#
+# de_dir<-gene_to_chr_file<-ct_file<-outDir<-data_cache_dir<- NULL
 
 #' Generate volcano plots for sex and age differential expression
 #'