MM-32: check if Y is vector and transpose if TRUE (#29)

R/MAPIT.R

@@ -76,6 +76,10 @@ MvMAPIT <- function(X,
     log$debug('Logging to file: %s', filePath)
     log$addHandler(logging::writeToFile, file=filePath)
   }
+
+  if (is.vector(Y)) {
+    Y <- t(Y)
+  }
 
   log$debug('Running in %s test mode.', test)
   log$debug('Genotype matrix: %d x %d', nrow(X), ncol(X))

tests/testthat/test-mvmapit-argument-parsing.R

@@ -0,0 +1,40 @@
+test_that("MvMapit can take a vector as phenotype input. hybrid = FALSE, test = normal", {
+  # given
+  p <- 10
+  n <- 4
+  pvalues <- matrix(rep(0.48001, 10), ncol = 1)
+  set.seed(853)
+  X <- matrix(runif(p * n), ncol = p)
+  Y <- c(runif(n))
+  # when
+  mapit <- MvMAPIT(t(X),
+                   Y,
+                   hybrid = FALSE,
+                   accuracy = 1e-5,
+                   cores = 1,
+                   phenotypeCovariance = 'identity',
+                   logLevel = "ERROR")
+  # then
+  expect_equal(mapit$pvalues, pvalues, tolerance = 1e-3)
+})
+
+test_that("MvMapit can take a vector as phenotype input. hybrid = FALSE, test = davies", {
+  # given
+  p <- 10
+  n <- 4
+  pvalues <- matrix(rep(0.209, 10), ncol = 1)
+  set.seed(853)
+  X <- matrix(runif(p * n), ncol = p)
+  Y <- c(runif(n))
+  # when
+  mapit <- MvMAPIT(t(X),
+                   Y,
+                   hybrid = FALSE,
+                   test = 'davies',
+                   accuracy = 1e-5,
+                   cores = 1,
+                   phenotypeCovariance = 'identity',
+                   logLevel = "ERROR")
+  # then
+  expect_equal(mapit$pvalues, pvalues, tolerance = 1e-3)
+})

tests/testthat/test-mvmapit-pariwise-executes-without-error.R

@@ -174,7 +174,6 @@ test_that("hybrid = FALSE, C is not NULL, test = 'davies'. phenotypeCovariance =
   expect_equal(mapit$pvalues, pvalues, tolerance = 1e-4)
 })
 
-
 test_that("hybrid = FALSE, test = 'davies'. phenotypeCovariance = '', d = 1", {
   # given
   p <- 10