v27

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

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)
- })
 
  }
 

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)
 }