MSnSet slots to SE metadata

lgatto · Dec 14, 2017 · 9fe34ff · 9fe34ff
1 parent b96dc91
commit 9fe34ff
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Showing 3 changed files with 66 additions and 24 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -69,8 +69,7 @@ Imports:
     S4Vectors,
     XML,
     scales,
-    Rcpp,
-    SummarizedExperiment
+    Rcpp
 Suggests:
     testthat,
     pryr,
@@ -92,7 +91,8 @@ Suggests:
     imputeLCMD,
     norm,
     gplots,
-    shiny
+    shiny,
+    SummarizedExperiment
 LinkingTo: Rcpp
 License: Artistic-2.0
 LazyData: yes

diff --git a/R/msnset2se.R b/R/msnset2se.R
@@ -11,10 +11,20 @@ setAs("MSnSet",
         rowData <- fData(from)
         colData <- pData(from)
 
+        # Extract metadata
+        metaData <- list(
+            processingData = processingData(from),
+            experimentData = experimentData(from),
+            protocolData = protocolData(from),
+            annotation = annotation(from),
+            qual = qual(from))
+
         # Generate SE
-        SummarizedExperiment(assays = as.matrix(raw),
+        SummarizedExperiment::SummarizedExperiment(
+            assays = as.matrix(raw),
             rowData = rowData,
-            colData = colData)
+            colData = colData,
+            metadata = metaData)
 })
 
 setAs("SummarizedExperiment",
@@ -26,12 +36,32 @@ setAs("SummarizedExperiment",
         }
 
         # Extract expression, feature and pheno data
-        raw <- assay(from)
-        featData <- data.frame(rowData(from), row.names = names(from))
-        phenoData <- data.frame(colData(from))
+        raw <- SummarizedExperiment::assay(from)
+        featData <- data.frame(
+            SummarizedExperiment::rowData(from), 
+            row.names = names(from))
+        phenoData <- data.frame(SummarizedExperiment::colData(from))
+
+        # Extract metadata
+        processingData = metadata(from)$processingData
+        experimentData = metadata(from)$experimentData
+        protocolData = metadata(from)$protocolData
+        annotation = metadata(from)$annotation
+        qual = metadata(from)$qual
 
         # Generate MSnSet
-        MSnSet(exprs = as.matrix(raw),
+        msnset <- MSnSet(exprs = as.matrix(raw),
             pData = AnnotatedDataFrame(phenoData),
             fData = AnnotatedDataFrame(featData))
-})
+        if(!is.null(experimentData)) 
+            msnset@experimentData <- experimentData
+        if(!is.null(processingData)) 
+            msnset@processingData <- processingData
+        if(!is.null(protocolData)) 
+            msnset@protocolData <- protocolData
+        if(!is.null(annotation)) 
+            msnset@annotation <- annotation
+        if(!is.null(qual)) 
+            msnset@qual <- qual
+        return(msnset)
+})
diff --git a/tests/testthat/test_msnset_se_coercions.R b/tests/testthat/test_msnset_se_coercions.R
@@ -1,15 +1,23 @@
 context("msnset - se conversion methods")
 
 test_that("msnset to se conversion", {
-	data(msnset, package = "MSnbase")
-	se <- as(msnset, "SummarizedExperiment")
-
-	expect_is(se, "SummarizedExperiment")
-	expect_equal(colnames(msnset), colnames(se))
-	expect_equal(rownames(msnset), rownames(se))
-	expect_equal(exprs(msnset), assay(se))
-	expect_equal(fData(msnset), data.frame(rowData(se), row.names = names(se)))
-	expect_equal(pData(msnset), data.frame(colData(se)))
+    data(msnset, package = "MSnbase")
+    se <- as(msnset, "SummarizedExperiment")
+
+    expect_is(se, "SummarizedExperiment")
+    expect_equal(colnames(msnset), colnames(se))
+    expect_equal(rownames(msnset), rownames(se))
+    expect_equal(
+        exprs(msnset), 
+        SummarizedExperiment::assay(se))
+    expect_equal(
+        fData(msnset), 
+        data.frame(
+            SummarizedExperiment::rowData(se), 
+            row.names = names(se)))
+    expect_equal(
+        pData(msnset), 
+        data.frame(SummarizedExperiment::colData(se)))
 })
 
 test_that("se to msnset conversion", {
@@ -18,9 +26,13 @@ test_that("se to msnset conversion", {
 	msnset_back <- as(se, "MSnSet")
 
 	expect_is(msnset_back, "MSnSet")
-	expect_equal(colnames(msnset_back), colnames(se))
-	expect_equal(rownames(msnset_back), rownames(se))
-	expect_equal(exprs(msnset_back), assay(se))
-	expect_equal(fData(msnset_back), data.frame(rowData(se), row.names = names(se)))
-	expect_equal(pData(msnset_back), data.frame(colData(se)))
+	expect_equal(colnames(msnset_back), colnames(msnset))
+	expect_equal(rownames(msnset_back), rownames(msnset))
+	expect_equal(exprs(msnset_back), exprs(msnset))
+	expect_equal(fData(msnset_back), fData(msnset))
+	expect_equal(pData(msnset_back), pData(msnset))
+	expect_equal(experimentData(msnset_back), experimentData(msnset))
+	expect_equal(protocolData(msnset_back), protocolData(msnset))
+	expect_equal(processingData(msnset_back), processingData(msnset))
+	expect_equal(qual(msnset_back), qual(msnset))
 })