Simplify 'motifMatrix', example data

R/motif-matrix.R

@@ -1,22 +1,36 @@
 motifMatrix <- function(vr, group = "sampleNames", normalize = TRUE) {
 
-    alteration = expand.grid(ref = DNA_BASES, alt = DNA_BASES)
-    alteration = subset(alteration, ref != alt & ref %in% c("C", "T"))
-    alteration = sort(paste0(alteration$ref, alteration$alt))
-    motifs = expand.grid(s = DNA_BASES, p = DNA_BASES, a = alteration)
-    motifs = sprintf("%s %s.%s", motifs$a, motifs$p, motifs$s)
-
-    df = as(unname(vr), "data.frame")
-    if(!(group %in% colnames(df))) {
-        stop(sprintf("Column '%s' not present in input object.", group))
+    voi <- if( group %in% names(mcols(vr)) ) {
+        mcols(vr)[ ,group]
+    } else {
+        df = as(unname(vr), "data.frame")
+        if( !(group %in% colnames(df)) ) {
+            stop(sprintf("Column '%s' not present in input object.", group))
+        }
+        df[ ,group]
     }
 
     ## form the matrix
-    df$motif = factor(paste(df$alteration, df$context), levels = motifs)
-    y = sapply(tapply(df$motif, df[ ,group], table), c)
+    motif = factor(paste(vr$alteration, vr$context),
+                   levels = constructMotifs3())
+    y = as(table(motif, voi), "matrix")
+    dimnames(y) = unname(dimnames(y))
 
-    if(normalize)
+    if(normalize) {
         y = t(t(y) / colSums(y))
+    }
 
     return(y)
 }
+
+
+constructMotifs3 <- function() {
+
+    alteration = expand.grid(ref = DNA_BASES, alt = DNA_BASES)
+    alteration = subset(alteration, ref != alt & ref %in% c("C", "T"))
+    alteration = sort(paste0(alteration$ref, alteration$alt))
+    motifs = expand.grid(s = DNA_BASES, p = DNA_BASES, a = alteration)
+    motifs = sprintf("%s %s.%s", motifs$a, motifs$p, motifs$s)
+
+    return(motifs)
+}

man/motif-functions.Rd

@@ -33,7 +33,7 @@ motifMatrix(vr, group = "sampleNames", normalize = TRUE)
   TRUE), the counts are transformed to frequencies, such that the sum of
   frequencies of each group equal 1.  Otherwise (with 'normalize' set to
   FALSE), the counts for each mofis in a group is returned.
-  
+
 }
 
 \value{
@@ -49,7 +49,7 @@ motifMatrix(vr, group = "sampleNames", normalize = TRUE)
 }
 
 \examples{
-\dontrun{
+data(sca_motifs_tiny)
+
 motifMatrix(sca_motifs, group = "study")
 }
-}

man/sca-data.Rd

@@ -3,6 +3,7 @@
 \alias{sca-data}
 \alias{sca_sigs}
 \alias{sca_mm}
+\alias{sca_motifs_tiny}
 \alias{sigs_nmf}
 \alias{sigs_pca}
 
@@ -26,6 +27,8 @@
 
 \examples{
 
+data(sca_motifs_tiny, package = "SomaticSignatures")
+
 data(sca_mm, package = "SomaticSignatures")
 
 data(sca_sigs, package = "SomaticSignatures")  

tests/testthat/test-SomaticSignatures.R

@@ -139,6 +139,8 @@ context("motifMatrix")
 
 test_that("'motifMatrix' works", {
 
+    data(sca_motifs_tiny)
+
     vr1 = readMutect(mutect_path)
     vr1 = mutationContextMutect(vr1)
     vr = readMutect(mutect_path, strip = TRUE)