Explicitly check upper bound of number of signatures

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SomaticSignatures
 Type: Package
 Title: Somatic Signatures
-Version: 2.7.3
+Version: 2.7.4
 Author: Julian Gehring (EMBL Heidelberg)
 Maintainer: Julian Gehring <[email protected]>
 Description: The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs).  It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

R/mutational-signatures.R

@@ -1,7 +1,7 @@
 identifySignaturesVRanges <- function(vr, group, nSigs, decomposition = nmfDecomposition, ...) {
 
     m = motifMatrix(vr, group, normalize = TRUE)
-    
+
     res = findSignatures(m, nSigs, decomposition, ...)
     res@decomposition = decomposition
     res@options = list(...)
@@ -21,12 +21,15 @@ identifySignatures <- function(m, nSigs, decomposition = nmfDecomposition, ...)
 findSignatures <- function(x, r, decomposition = nmfDecomposition, ...) {
 
     ## check input arguments
-    if(!( length(r) == 1 & all.equal(r, as.integer(r)) & r > 0 ))
-        stop("'nSigs | r' must be a single, positive integer.")
+    nm = min(dim(x))
+    if(!( length(r) == 1 & all.equal(r, as.integer(r)) & r > 0 & r <= nm)) {
+        msg = "'nSigs | r' must be a single, positive integer in the range [1,%d]"
+        stop(sprintf(msg, nm))
+    }
 
     if(!is.function(decomposition))
         stop("'decomposition' must be a function.")
-    
+
     dc = decomposition(x, r, ...)
 
     ## check returned object
@@ -36,7 +39,7 @@ findSignatures <- function(x, r, decomposition = nmfDecomposition, ...) {
             paste(required_names, ", "))
         stop(msg)
     }
-    
+
     res = new("MutationalSignatures",
         signatures = dc$w,
         samples = dc$h,

tests/testthat/test-SomaticSignatures.R

@@ -142,7 +142,7 @@ test_that("'motifMatrix' works", {
 
     data(sca_motifs_tiny)
     vr = sca_motifs_tiny
-  
+
     mm = motifMatrix(vr, "study")
 
     expect_equal( nrow(mm), 96 )
@@ -178,6 +178,10 @@ test_that("'identifySignatures' handles bad inputs", {
     expect_error( identifySignatures(sca_mm, 0),
                  ".*single, positive integer.*")
 
+    ## bad number of signatures
+    expect_error( identifySignatures(sca_mm, min(dim(sca_mm))+1),
+                 ".*in the range.*")
+
     ## 'decomposition' argument no function
     expect_error( identifySignatures(sca_mm, 3, "a"),
                  "*.must be a function.*")
@@ -203,6 +207,16 @@ test_that("'assessNumberSignatures' works", {
 
 })
 
+test_that("'assessNumberSignatures' handles bad inputs", {
+
+    data("sca_mm", package = "SomaticSignatures")
+
+    nm = min(dim(sca_mm))
+    expect_error( assessNumberSignatures(sca_mm, (nm-1):(nm+2)),
+                 ".*in the range.*")
+
+})
+
 test_that("'assessNumberSignatures' low-level functions work", {
 
     x = matrix(rnorm(100, 20))