From 14fdbea98b039699aeea8b849a29234de5f2e50c Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Sat, 22 Mar 2025 09:58:09 -0400
Subject: [PATCH] Update colocboost_pipeline.R

add a hard-code part to remove the rare events from list. will be removed later.
---
 R/colocboost_pipeline.R | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/R/colocboost_pipeline.R b/R/colocboost_pipeline.R
index 1d013ae9..e73c2272 100644
--- a/R/colocboost_pipeline.R
+++ b/R/colocboost_pipeline.R
@@ -106,6 +106,41 @@ load_multitask_regional_data <-  function(region, # a string of chr:start-end fo
         stop("Data load error. Please make sure at least one data set (sumstat_path_list or genotype_list) exists.")
     }
     
+    # FIXME: hard_code: remove rare events
+    add_hoc_remove_rare_events <- function(events_name, rare_events_path){
+        clean_events_name <- gsub(":ENSG[0-9]+", "", events_name)
+        rare_events <- read.table(rare_events_path, header = T)$ID
+        rare <- intersect(rare_events, clean_events_name)
+        if (length(rare)!=0&length(rare)!=length(clean_events_name)){
+            message(paste("Remove", length(rare), "rare events out of", length(clean_events_name), "events"))
+            pp <- match(rare, clean_events_name)
+            return(events_name[-pp])
+        } else if (length(rare)==length(clean_events_name)){
+            message(paste("Remove rare events for all", length(clean_events_name), "events"))
+            return(NULL)
+        } else {
+            message("No rare events")
+            return(events_name)
+        }
+    }
+    brain_region <- c("AC", "DLPFC", "PCC")
+    for (rr in brain_region){
+      tmp <- paste0(rr, "_lf2_sQTL")
+      if ( !(tmp %in% conditions_list_individual) ) next
+      pos <- which(conditions_list_individual == tmp)
+      rare_events_path = paste0("/home/xc2270/COLOCBoost/pipeline/ROSMAP_", rr, 
+                                "_perind.counts.noise_by_intron.QCed_minc1_mins10.NOTpass_rare_filtered_0.9.ID_list")
+      remain_events <- add_hoc_remove_rare_events(extract_region_name[[pos]], rare_events_path)
+      if (!is.null(remain_events)){
+          extract_region_name[[pos]] <- remain_events
+      } else {
+          conditions_list_individual <- conditions_list_individual[-pos]
+          extract_region_name <- extract_region_name[-pos]
+          phenotype_list <- phenotype_list[-pos]
+          covariate_list <- covariate_list[-pos]
+      }
+    }
+    
     # - if exist individual level data
     individual_data <- NULL
     if (!is.null(genotype_list)){