Updated replicate filtering to detect replicates in CpGs with non-sta…

…ndard names

scripts/6_filtering_cpgs.Rmd

@@ -59,7 +59,7 @@ We will remove probes that:
 * cross-hybridize as described by McCartney et al. (v1.0 only)    
 * are polymorphic (v1.0 only)  
 * show mapping inaccuracies or were flagged by Illumina (v2 only) 
-Please note: replicate removal is performed for the filtered AND unfiltered data (v2 only.  
+Please note: replicate removal is performed for the filtered AND unfiltered data (v2 only).  
 
 ```{r get annotation of probes, include=FALSE}
 annotations_clean = getAnnotation(RGSet_clean)
@@ -73,19 +73,19 @@ if (user_choices$array_type == "v2") {
   # add non-unique CpG name
   CpG_names <- as.data.frame(rownames(Betas_clean))
   colnames(CpG_names) <- c("IlmnID")
-  CpG_names$CpG_name <- str_sub(CpG_names$IlmnID, 1, 10)
+  CpG_names$CpG_name <- sub("\\_.*", "", CpG_names$IlmnI)
+  # CpG_names$CpG_name <- str_sub(CpG_names$IlmnID, end = -6)
   # isolate replicate IDs
   replicates <- CpG_names %>%
-    group_by(CpG_name) %>%
-    filter(n()>1) %>% 
+    filter(duplicated(CpG_name)) %>% 
     distinct(CpG_name)
   
   # link to detP values
   CpG_names_detP <- left_join(CpG_names, as.data.frame(cbind(rownames(detP_clean), 
                                                              rowMeans(detP_clean))), by = join_by("IlmnID" == "V1"))
   colnames(CpG_names_detP) <- c("IlmnID", "CpG_name", "detP_value")
   
-  cat(paste0(nrow(replicates), " replicate CpGs were detected"))
+  cat(paste0(nrow(replicates), " CpGs with one or more replicates were detected"))
   }
 ```
 
@@ -98,12 +98,12 @@ if (user_choices$array_type == "v2") {
     slice_min(detP_value) %>%
     ungroup() 
   keep_replicates <- keep_replicates %>%
-    filter(duplicated(CpG_name) == FALSE)
+    filter(!duplicated(CpG_name))
   
   # create list of replicates to exclude (CpGs in replicate list but probe not in keep list)
   exclude_replicates <- CpG_names_detP %>%
     filter(CpG_name %in% replicates$CpG_name) %>%
-    filter(!(IlmnID %in% keep_replicates$IlmnID))
+    filter(!IlmnID %in% keep_replicates$IlmnID)
   
   # exclude replicates from betas, gRatioSet, detP and save data
   keep_gratioset <- !(featureNames(gRatioSet_clean) %in% exclude_replicates$IlmnID)