fix: solved bug in DA when missing contrast level in modelled feature

NEWS.md

@@ -1,5 +1,10 @@
 # scp 1.15
 
+## scp 1.15.2
+
+- fix: solved bug in DA when missing contrast level in modelled 
+  feature (issue #65).
+
 ## scp 1.15.1
 
 - test: added unit tests for scplainer: ScpModel-Class, 

R/ScpModel-DifferentialAnalysis.R

@@ -249,32 +249,37 @@ scpDifferentialAnalysis <- function(object,
 
 ## Internal function that takes a contrast and retrieves the estimated
 ## log fold change and associated standard error between the two
-## defined groups. The inference is performed on the model coefficients
-## and the variance covariance matrix that are automatically retrieved
-## from the SummarizedExperimeent object. The log fold change and the
-## standard error are returned for all features in a list.
+## defined groups. The inference is performed on the model
+## coefficients and the variance covariance matrix that are
+## automatically retrieved from the SummarizedExperimeent object. The
+## log fold change and the standard error are returned for all
+## features in a list.
+##
+## Note that the function may return NA estimates for features where
+## missing data leads to loss of one or two levels of interest
+## supplied by `contrast`.
 ##
 ## @param object An object that inherits from the
-##     `SummarizedExperiment` class. It must contain an estimated
-##     `ScpModel` in its metadata.
-## @param contrast A `character(3)` with the following elements: 1. The
-##     name of a categorical variable to test; 2. The name of the
-##     reference group: 3. The name of the second group to contrast
-##     against the reference group. `coefficients` and `contrasts`
-##     cannot be both NULL.
+##   `SummarizedExperiment` class. It must contain an estimated
+##   `ScpModel` in its metadata.
+## @param contrast A `character(3)` with the following elements: 1.
+##   The name of a categorical variable to test; 2. The name of the
+##   reference group: 3. The name of the second group to contrast
+##   against the reference group. `coefficients` and `contrasts`
+##   cannot be both NULL.
 ## @param name A `character(1)` providing the name to use to retrieve
-##     the model results. When retrieving a model and `name` is
-##     missing, the name of the first model found in `object` is used.
+##   the model results. When retrieving a model and `name` is missing,
+##   the name of the first model found in `object` is used.
 ##
-## cf https://stats.stackexchange.com/a/446699
+##   cf https://stats.stackexchange.com/a/446699
 .contrastToEstimates <- function(object, contrast, name) {
     fits <- scpModelFitList(object, name, filtered = TRUE)
     out <- sapply(fits, function(fit) {
         coef <- scpModelFitCoefficients(fit)
         vcov <- scpModelFitVcov(fit)
         levs <- scpModelFitLevels(fit)[[contrast[[1]]]]
-        if (length(levs) <= 1) return(c(logFc = NA, se = NA))
         contrastMat <- .levelsToContrastMatrix(contrast, levs)
+        if (is.null(contrastMat)) return(c(logFc = NA, se = NA))
         sel <- grepl(contrast[[1]], names(coef))
         logFc <- contrastMat %*% coef[sel]
         se <- sqrt(contrastMat %*% vcov[sel, sel] %*% t(contrastMat))
@@ -289,20 +294,22 @@ scpDifferentialAnalysis <- function(object,
 ## the quantification of the log fold change between the 2 groups of
 ## interest.
 ##
-## If one of the levels is absent in contrast (happens when a level
-## has been dropped during modelling), the function return NA.
+## If `levels` contains only a single level or if one of the levels
+## requested in `contrast` is absent (happens when a level has been
+## dropped during modelling), the function return NULL since no
+## contrast matrix can be computed.
 ##
-## @param contrasts A `character(3)` with the following elements: 1. The
-##     name of a categorical variable to test; 2. The name of the
-##     reference group: 3. The name of the second group to contrast
-##     against the reference group. `coefficients` and `contrasts`
-##     cannot be both NULL.
+## @param contrasts A `character(3)` with the following elements: 1.
+##   The name of a categorical variable to test; 2. The name of the
+##   reference group: 3. The name of the second group to contrast
+##   against the reference group. `coefficients` and `contrasts`
+##   cannot be both NULL.
 ## @param levels A `character()` containing all possible levels
-##     contained by the model variable identified by contrast[[1]].
+##   contained by the model variable identified by contrast[[1]].
 ##
 .levelsToContrastMatrix <- function(contrast, levels) {
-    if (any(!contrast[2:3] %in% levels))
-        return(structure(NA, .Names = contrast[[1]]))
+    if (length(levels) <= 1 || any(!contrast[2:3] %in% levels))
+        return(NULL)
     df <- data.frame(group = factor(levels, levels = levels))
     mm <- model.matrix(
         ~ 1 + group, data = df,

tests/testthat/test-ScpModel-DifferentialAnalysis.R

@@ -409,25 +409,68 @@ test_that(".contrastToEstimates", {
         ),
         tolerance = 1E-2
     )
+    ## Test when a level of interest is dropped for a 2-level variable
+    se <- .createMinimalData(nr = 2, nc = 10)
+    se$condition1 <- as.factor(rep(1:2, length.out = ncol(se)))
+    se$condition2 <- as.factor(rep(1:2, each = 5))
+    assay(se)[, se$condition1 == 2] <- 10 * assay(se)[, se$condition1 == 2]
+    ## Drop one level of condition2 for first row, second row is
+    ## positive control.
+    assay(se)[1, se$condition2 == 2] <- NA
+    se <- scpModelWorkflow(se, formula = ~ 1 + condition1 + condition2)
+    expect_equal(
+        .contrastToEstimates(
+            se, contrast = c("condition2", "1", "2"), name = "model"
+        ),
+        list(logFc = c(a = NA, b = 0.0001874609),
+             se = c(a = NA, b  = 0.0005527098)),
+        tolerance = 1E-6
+    )
+    ## Test when a level of interest is dropped for a 3-level variable
+    se <- .createMinimalData(nr = 2, nc = 12)
+    se$condition1 <- as.factor(rep(1:2, length.out = ncol(se)))
+    se$condition2 <- as.factor(rep(1:3, each = 4))
+    assay(se)[, se$condition1 == 2] <- 10 * assay(se)[, se$condition1 == 2]
+    ## Drop one level of condition2 for first row, second row is
+    ## positive control.
+    assay(se)[1, se$condition2 == 2] <- NA
+    se <- scpModelWorkflow(se, formula = ~ 1 + condition1 + condition2)
+    expect_equal(
+        .contrastToEstimates(
+            se, contrast = c("condition2", "1", "2"), name = "model"
+        ),
+        list(logFc = c(a = NA, b = 0),
+             se = c(a = NA, b  = 0.0005126847)),
+        tolerance = 1E-6
+    )
+    ## Make sure the contrast for remaining levels is still estimated
+    expect_equal(
+        .contrastToEstimates(
+            se, contrast = c("condition2", "1", "3"), name = "model"
+        ),
+        list(logFc = c(a = 0, b = 0),
+             se = c(a = 0.0007943138, b = 0.0005127487 )),
+        tolerance = 1E-6
+    )
 })
 
 test_that(".levelsToContrastMatrix", {
-    ## 1 level or less = NA
-    expect_error(
+    ## 1 level or less = NULL
+    expect_identical(
         .levelsToContrastMatrix(contrast = c("condition", "A", "B"),
                                 levels = "A"),
-        NA
+        NULL
     )
-    expect_error(
+    expect_identical(
         .levelsToContrastMatrix(contrast = c("condition", "A", "B"),
                                 levels = character()),
-        NA
+        NULL
     )
     ## 1 level to test is not in available levels = NA
-    expect_error(
+    expect_identical(
         .levelsToContrastMatrix(contrast = c("condition", "A", "foo"),
                                 levels = c("A", "B")),
-        NA
+        NULL
     )
     ## 2-level variable
     expect_identical(