Merge pull request #13 from Aggarwal-Ayush/master

Rectified Issue #11: specifying chromosome does not map aliases if gene is correct on another chromosome
waldronlab · Jan 20, 2021 · 2d42d2b · 2d42d2b
2 parents 177b3c8 + c96df92
commit 2d42d2b
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diff --git a/R/checkGeneSymbols.R b/R/checkGeneSymbols.R
@@ -103,6 +103,14 @@ checkGeneSymbols <- function(x,
 
   approved <- x %in% map$Approved.Symbol
 
+  if (!is.null(chromosome)) {
+    approved.chr <- sapply(1:length(chromosome), function(i)
+      ifelse(chromosome[i] %in% unique(map[map$Approved.Symbol %in% x[i], chromosome]), 
+             TRUE, 
+             FALSE))
+    approved <- approved & approved.chr
+  }
+
   if (identical(species, "human")) {
     # change to uppercase, then change orfs back to lowercase
     x.casecorrected <- toupper(x)

diff --git a/tests/testthat/test_checkGeneSymbols.R b/tests/testthat/test_checkGeneSymbols.R
@@ -62,6 +62,13 @@ expect_equal(res[,3], c("GEMIN2", "SCAF11", "GEMIN2 /// SCAF11 /// ZEB2"))
 expect_equal(res[,4], c(14, 12, 3))
 expect_equal(res[,5], c("14", "12", "14 /// 12 /// 2"))
 
+# approved symbol alias mapping on different chromosome
+expect_warning(res <- checkGeneSymbols(c("TKT", "FFM","ABCA4", "TKT", "AAVS1"), chromosome = c(1, 1, 1, 3, 19)), 
+               "x contains non-approved gene symbols") 
+expect_equal(res[,2], c(FALSE, FALSE, TRUE, TRUE, TRUE))
+expect_equal(res[,3], c("DDR2", "ABCA4", "ABCA4", "TKT", "AAVS1"))
+expect_equal(res[,4], c(1, 1, 1, 3, 19))
+expect_equal(res[,5], c(1, 1, 1, 3, 19))
 
 
 ## mouse test 1