map_df_to_list() - ensure output has numeric positions

- Fixes Issue #17.
rqtl · Sep 21, 2019 · 5ad341b · 5ad341b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qtl2convert
-Version: 0.20
-Date: 2019-06-03
+Version: 0.21-1
+Date: 2019-09-21
 Title: Convert Data among R/qtl2, R/qtl, and DOQTL
 Description: Functions to convert data structures among the R/qtl2, R/qtl, and DOQTL packages.
 Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+## qtl2convert 0.21 (2019-09-21)
+
+- Have `map_df_to_list()` ensure that the positions in the output are
+  numeric.
+
+
 ## qtl2convert 0.20 (2019-06-03)
 
 - Use Markdown for function documentation, throughout

diff --git a/R/map_df_to_list.R b/R/map_df_to_list.R
@@ -47,7 +47,7 @@ map_df_to_list <-
     uchr <- unique(chr)
     pos <- map[,pos_column]
 
-    result <- split(pos, factor(chr, levels=uchr))
+    result <- split(as.numeric(pos), factor(chr, levels=uchr))
     marker <- split(marker, factor(chr, levels=uchr))
     for(i in seq(along=result))
         names(result[[i]]) <- marker[[i]]

diff --git a/tests/testthat/test-map_df_to_list.R b/tests/testthat/test-map_df_to_list.R
@@ -42,4 +42,28 @@ test_that("map_df_to_list works", {
 
     expect_equal(map_df_to_list(df), expected)
 
+
+    # same thing with character string positions in the input
+    df <-  structure(list(marker = c("JAX00240989", "JAX00240649", "UNCJPD009180",
+                          "JAX00240804", "JAX00240610", "UNCHS003854", "UNCHS003852", "UNCHS003846",
+                          "JAX00482049", "JAX00482064", "JAX00281864", "ICR260", "JAX00014570",
+                          "JAX00281798", "ICR4249", "JAX00708681", "JAX00708630r", "UNCHS048201",
+                          "JAX00176676", "UNCHS048205"), chr = c("1", "1", "1", "1", "1",
+                                                         "2", "2", "2", "2", "2", "10", "10", "10",
+                                                         "10", "10", "X", "X", "X", "X", "X"),
+                          Mb_GRC38 = c("5.379217", "3.454984", "5.754074", "4.334891",
+                          "3.266608", "4.118437", "4.115724", "3.74537", "3.23375", "3.362696", "4.306508",
+                          "3.5931", "3.993759", "4.631578", "4.666669", "6.845222", "6.369421", "6.536718",
+                          "6.05422", "6.586892"),
+                          cM = c("0.424118388815167", "0.041241020125091",
+                          "0.466051450603133", "0.0654810203913158", "0.0241660935186957", "0.182846980321827",
+                          "0.182407517001796", "0.130917988391064", "0.000412833594312019", "0.000640569383198255",
+                          "0.0163163877989646", "0.00740695778637858", "0.0124106069176088",
+                          "0.0203760400795549", "0.0208142757155046", "0.827432787823843", "0.235740657791282",
+                          "0.397500188730613", "0.0507409752570731", "0.501406880974154")),
+                     .Names = c("marker", "chr", "Mb_GRC38", "cM"), class = "data.frame",
+                     row.names = c(NA, -20L))
+
+    expect_equal(map_df_to_list(df), expected)
+
 })