Add checks for missing non-reference samples (all samples missing, so…

…me samples missing) in the merged dataset (addressing issue #28).
meyer-lab-cshl · Jul 7, 2020 · 5c03971b92341b5a8cb26a1d5f2e37d637f5cbd7 · 5c03971
1 parent 0ecd60b
commit 5c03971b92341b5a8cb26a1d5f2e37d637f5cbd7
Unified Split

Showing with 2,580 additions and 0 deletions.

+8 −0 R/individualQC.R

+1,184 −0 tests/testthat/data.HapMapIII_no_samples.eigenvec

+1,375 −0 tests/testthat/data.HapMapIII_some_samples.eigenvec

+13 −0 tests/testthat/test-individualQC.R
diff --git a/R/individualQC.R b/R/individualQC.R
@@ -1882,6 +1882,14 @@ evaluate_check_ancestry <- function(indir, name, prefixMergedDataset,
                                   stringsAsFactors=FALSE, data.table=FALSE)
     colnames(pca_data) <- c("FID", "IID", paste("PC",1:(ncol(pca_data)-2),
                                                 sep=""))
+    if (!any(samples$IID %in% pca_data$IID)) {
+        stop("There are no ", prefix, ".fam samples in the prefixMergedDataset")
+    }
+    if (!all(samples$IID %in% pca_data$IID)) {
+        stop("Not all ", prefix, ".fam samples are present in the",
+             "prefixMergedDataset")
+    }
+
     #pca_data$IID <- as.character(pca_data$IID)
     #pca_data$FID <- as.character(pca_data$FID)