Add midp modifier for --hwe and --hardy as recommended on [plink hwe …

…documentation](https://www.cog-genomics.org/plink/1.9/filter#hwe) and discussed in issue #27.
meyer-lab-cshl · Aug 5, 2020 · d009da9 · d009da9
1 parent 5c9cd4c
commit d009da9
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/R/applyQC.R b/R/applyQC.R
@@ -266,7 +266,7 @@ cleanData <- function(indir, name, qcdir=indir,
         if (is.null(hweTh)) {
             stop("filterHWE is TRUE but hweTh not specified")
         } else {
-           hwe <- c("--hwe", hweTh)
+           hwe <- c("--hwe midp", hweTh)
         }
     }
     if (filterMAF) {

diff --git a/R/markerQC.R b/R/markerQC.R
@@ -436,7 +436,7 @@ check_hwe <- function(indir, name, qcdir=indir, hweTh=1e-5, interactive=FALSE,
         }
         suffix <- ""
         sys::exec_wait(path2plink,
-                       args=c("--bfile", prefix, "--hardy", "--out",
+                       args=c("--bfile", prefix, "--hardy midp", "--out",
                               paste(out, suffix, sep="")),
                     std_out=showPlinkOutput, std_err=showPlinkOutput)
     } else {