From 0fe332bfcec90197126b22dbc1caebf94c183181 Mon Sep 17 00:00:00 2001
From: Nicholas Sunderland <nicholas.p.sunderland@gmail.com>
Date: Wed, 11 Sep 2024 13:31:20 +0100
Subject: [PATCH] v27

---
 DESCRIPTION    |  2 +-
 R/class_gwas.R |  6 ------
 R/plink.R      | 14 ++++++++------
 3 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e8c6498..36ac295 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: genepi.utils
 Title: GenEpi Utility Functions
-Version: 0.0.26
+Version: 0.0.27
 Authors@R: c(person("Nicholas", "Sunderland", , "nicholas.sunderland@bristol.ac.uk", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3625-630X")))
 Description: The genepi.utils package is a collection of utility functions for working with genetic epidemiology data.
 License: MIT + file LICENSE
diff --git a/R/class_gwas.R b/R/class_gwas.R
index a1cb7c2..f9b43e9 100644
--- a/R/class_gwas.R
+++ b/R/class_gwas.R
@@ -892,7 +892,6 @@ method(get_proxies, GWAS) <- function(x,
   } else {
     message(paste0("[i] ", length(missing), "/", length(snps), " (", sprintf("%.2f", 100*(length(missing)/length(snps))), "%) missing variants"))
 
-    tryCatch({
 
       # search for proxies for the missing SNPs
       proxies <- get_proxies(missing,
@@ -954,11 +953,6 @@ method(get_proxies, GWAS) <- function(x,
 
         return(object)
       })
-    },
-    error = function(e) {
-      warning("Getting proxies failed, returning original GWAS object")
-      return(x)
-    })
 
   }
 
diff --git a/R/plink.R b/R/plink.R
index d8586b4..642583e 100644
--- a/R/plink.R
+++ b/R/plink.R
@@ -181,6 +181,9 @@ method(get_proxies, class_character) <- function(x,
   # read the found SNPs
   snps_exist <- data.table::fread(paste0(exists_file,".pvar"), skip="#CHROM	POS	ID	REF	ALT", select=c("ID"))
 
+  # clean up
+  unlink(paste0(exists_file,".pvar"))
+
   # report
   message(paste0("[i] ", nrow(snps_exist), "/", length(x), " (", sprintf("%.1f", 100*(nrow(snps_exist)/length(x))), "%) input SNPs found in plink reference file"))
 
@@ -203,8 +206,7 @@ method(get_proxies, class_character) <- function(x,
   system(cmd)
 
   if (!file.exists(paste0(proxy_file,".vcor"))) {
-    warning("No variants found, or plink failed")
-    return(NULL)
+    stop(paste0("Plink `", paste0("--", stat), "` failed"))
   }
 
   # read in the extracted variants file
@@ -224,6 +226,10 @@ method(get_proxies, class_character) <- function(x,
                             proxy_freq_alt = as.numeric(NONMAJ_FREQ_B),
                             rstat          = as.numeric(get(names(which(stats == stat)))))]
 
+  # clean up
+  unlink(paste0(proxy_file,".vcor"))
+  unlink(snps_found)
+
   # filter on eaf
   if (!is.null(proxy_eaf)) {
     nproxies <- nrow(proxies)
@@ -233,10 +239,6 @@ method(get_proxies, class_character) <- function(x,
     }
   }
 
-  # clean up
-  unlink(paste0(exists_file,".pvar"))
-  unlink(paste0(proxy_file,".vcor"))
-
   return(proxies)
 }