replace refDosage() by imputedDosage() to read DS from format

UW-GAC · Nov 24, 2024 · 12492df · 12492df
1 parent dd2a91b
commit 12492df
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,5 @@
 ^renv$
 ^renv\.lock$
 ^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/R/admixMap.R b/R/admixMap.R
@@ -81,7 +81,9 @@ admixMap <- function(admixDataList,
             if (is(admixDataList[[1]], "GenotypeIterator")) {
                 local[,,i] <- getGenotypeSelection(admixDataList[[i]], scan=sample.index, order="selection", transpose=TRUE, use.names=FALSE, drop=FALSE)
             } else {
-                local[,,i] <- refDosage(admixDataList[[i]], use.names=FALSE)[sample.index,,drop=FALSE]
+               # local[,,i] <- refDosage(admixDataList[[i]], use.names=FALSE)[sample.index,,drop=FALSE]
+               local[,,i] <- imputedDosage(admixDataList[[i]], use.names=FALSE)[sample.index,,drop=FALSE]
+
             }
         }
         if (any(is.na(local))) warning("missing values in local ancestry will produce NA output for this block")