add fold change tests

Author: grlloyd

tests/testthat/test-foldchange.R

@@ -0,0 +1,64 @@
+# fold_change
+test_that('fold_change',{
+  set.seed('57475')
+  
+  # data
+  D = iris_DatasetExperiment()
+  
+  # two groups
+  F = filter_smeta(mode='exclude',levels='setosa',factor_name='Species')
+  F = model_apply(F,D)
+  
+  D = predicted(F)
+  
+  # add column for paired data
+  D$sample_meta$sample_id=c(1:50,1:50)
+  D$data[1:50,2] = NA
+  D$data[1:25,3] = NA
+  
+  # unpaired
+  FF = fold_change(factor_name='Species',method="geometric")
+  FF = model_apply(FF,D)
+  m=exp(mean(log(D$data[D$sample_meta$Species=='virginica',1]))) / exp(mean(log((D$data[D$sample_meta$Species=='versicolor',1]))))
+  expect_equal(FF$fold_change[1,1],m,tolerance=0.00001)
+  expect_true(is.na(FF$fold_change[2,1]))
+  m=exp(mean(log(na.exclude(D$data[D$sample_meta$Species=='virginica',3])))) / exp(mean(log(na.exclude(D$data[D$sample_meta$Species=='versicolor',3]))))
+  expect_equal(FF$fold_change[3,1],m,tolerance=0.00001)
+  
+  FF$method = 'median'
+  FF = model_apply(FF,D)
+  m = median(D$data[D$sample_meta$Species=='virginica',1]) / median(D$data[D$sample_meta$Species=='versicolor',1])
+  expect_equal(FF$fold_change[1,1],m,tolerance=0.00001)
+  expect_true(is.na(FF$fold_change[2,1]))
+  m = median(D$data[D$sample_meta$Species=='virginica',3],na.rm = TRUE) / median(D$data[D$sample_meta$Species=='versicolor',3],na.rm = TRUE)
+  expect_equal(FF$fold_change[3,1],m,tolerance=0.00001)
+  
+  FF$method = 'mean'
+  FF = model_apply(FF,D)
+  m = mean(D$data[D$sample_meta$Species=='virginica',1]) / mean(D$data[D$sample_meta$Species=='versicolor',1])
+  expect_equal(FF$fold_change[1,1],m,tolerance=0.00001)
+  expect_true(is.na(FF$fold_change[2,1]))
+  m = mean(D$data[D$sample_meta$Species=='virginica',3],na.rm=TRUE) / mean(D$data[D$sample_meta$Species=='versicolor',3],na.rm=TRUE)
+  expect_equal(FF$fold_change[3,1],m,tolerance=0.00001)
+  
+  # paired
+  FF = fold_change(factor_name='Species',method="geometric",paired=TRUE,sample_name = 'sample_id')
+  FF = model_apply(FF,D)
+  m=exp(mean(log(D$data[D$sample_meta$Species=='virginica',1])-log(D$data[D$sample_meta$Species=='versicolor',1])))
+  expect_equal(FF$fold_change[1,1],m,tolerance=0.00001)
+  expect_true(is.na(FF$fold_change[2,1]))
+  
+  FF$method = 'median'
+  FF = model_apply(FF,D)
+  m = median(D$data[D$sample_meta$Species=='virginica',1] / D$data[D$sample_meta$Species=='versicolor',1])
+  expect_equal(FF$fold_change[1,1],m,tolerance=0.00001)
+  expect_true(is.na(FF$fold_change[2,1]))
+  
+  FF$method = 'mean'
+  FF = model_apply(FF,D)
+  m = mean(D$data[D$sample_meta$Species=='virginica',1] / D$data[D$sample_meta$Species=='versicolor',1])
+  expect_equal(FF$fold_change[1,1],m,tolerance=0.00001)
+  expect_true(is.na(FF$fold_change[2,1]))
+
+
+})