bug fix: order of flow for imp SNP with imp col

Al-Murphy · Jul 17, 2023 · 7f292ca · 7f292ca
1 parent 8df9b70
commit 7f292ca
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: MungeSumstats
 Type: Package
 Title: Standardise summary statistics from GWAS
-Version: 1.9.11
+Version: 1.9.12
 Authors@R:
     c(person(given = "Alan",
            family = "Murphy",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+## CHANGES IN VERSION 1.9.12
+
+### Bug fix
+* In `check_no_rs_snp` the order of operations had to be reversed to ensure all 
+values were present before sorting column headers when `imputation_ind=TRUE` and
+imputing rsIDs.
+
 ## CHANGES IN VERSION 1.9.11
 
 ### New features

diff --git a/R/check_no_rs_snp.R b/R/check_no_rs_snp.R
@@ -264,14 +264,14 @@ check_no_rs_snp <- function(sumstats_dt, path, ref_genome, snp_ids_are_rs_ids,
                     miss_rs_chr_bp[, "SNP"]), ]
                 # remove temp columns
                 miss_rs_chr_bp[, (format) := NULL]
-                # get columns in same order as rest of data table
-                data.table::setcolorder(miss_rs_chr_bp, col_headers)
                 # join with full dataset
                 # If IMPUTATION column added add it to other DT
                 if (imputation_ind &&
                     !"IMPUTATION_SNP" %in% names(miss_rs_chr_bp)) {
                     miss_rs_chr_bp[, IMPUTATION_SNP := NA]
                 }
+                # get columns in same order as rest of data table
+                data.table::setcolorder(miss_rs_chr_bp, col_headers)
                 sumstats_dt <- data.table::rbindlist(
                     list(sumstats_dt, miss_rs_chr_bp))
             }