Merge pull request #241 from imbs-hl/gwaa_prediction

fix prediction for GenABEL data without covars
imbs-hl · Nov 29, 2017 · f3a1a31 · f3a1a31
2 parents 77b84be + 12469c8
commit f3a1a31
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/R/predict.R b/R/predict.R
@@ -79,7 +79,7 @@ predict.ranger.forest <- function(object, data, predict.all = FALSE,
   if ("gwaa.data" %in% class(data)) {
     snp.names <- snp.names(data)
     snp.data <- data@gtdata@gtps@.Data
-    data <- data@phdata[, -1]
+    data <- data@phdata[, -1, drop = FALSE]
     gwa.mode <- TRUE
     variable.names <- c(names(data), snp.names)
   } else {

diff --git a/tests/testthat/test_ranger.R b/tests/testthat/test_ranger.R
@@ -210,3 +210,10 @@ test_that("No error if variable named forest", {
   rf <- ranger(Species ~ ., dat, num.trees = 5)
   expect_silent(predict(rf, dat))
 })
+
+test_that("GenABEL prediction works if no covariates and formula used", {
+  dat <- dat.gwaa
+  dat@phdata$Age <- NULL
+  rf <- ranger(CHD ~ .-Sex, data = dat, num.trees = 5)
+  expect_silent(predict(rf, dat))
+})