fixed ld extraction in run_carma

mglev1n · Mar 16, 2024 · f6f72dd · f6f72dd
1 parent 9d38a3c
commit f6f72dd
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/R/run_carma.R b/R/run_carma.R
@@ -27,8 +27,10 @@ run_carma <- function(df, snp_col, z_col, effect_allele_col, bfile, threads = 1,
 
   sumstat <- df
 
+  plink_extract_ld_possibly <- purrr::possibly(levinmisc::plink_extract_ld) 
+
   ld <- df %>%
-    plink_extract_ld(bfile = bfile, snp_col = {{snp_col}}, effect_allele_col = {{effect_allele_col}})
+    plink_extract_ld_possibly(bfile = bfile, plink_bin = plink_bin, snp_col = {{snp_col}}, effect_allele_col = {{effect_allele_col}})
 
   if(is.null(ld)) {
     return(sumstat %>% mutate(ld_error = TRUE))

diff --git a/dev/flat_genomics_functions.Rmd b/dev/flat_genomics_functions.Rmd
@@ -921,8 +921,10 @@ run_carma <- function(df, snp_col, z_col, effect_allele_col, bfile, threads = 1,
   
   sumstat <- df
   
+  plink_extract_ld_possibly <- purrr::possibly(levinmisc::plink_extract_ld) 
+  
   ld <- df %>%
-    plink_extract_ld(bfile = bfile, snp_col = {{snp_col}}, effect_allele_col = {{effect_allele_col}})
+    plink_extract_ld_possibly(bfile = bfile, plink_bin = plink_bin, snp_col = {{snp_col}}, effect_allele_col = {{effect_allele_col}})
   
   if(is.null(ld)) {
     return(sumstat %>% mutate(ld_error = TRUE))