Changed processAssayXcmsSet methods, eliminating for loop, added new …

…term for isatab.syntax

R/Risa-ms.R

@@ -3,41 +3,39 @@
 ### specific function to deal with assays whose technology type is mass spectrometry using the xcms package
 ### it returns an xcmsSet
 processAssayXcmsSet.1factor = function(isa, assay.filename, ...){
-  for(i in seq_len(length(isa["assay.filenames"]))){
+
+  i <- which(isa["assay.filenames"]==assay.filename)
+
+  if (isatab.syntax$raw.spectral.data.file %in% colnames(isa["data.filenames"][[i]]))
+  {
+    #mass spectrometry files
+    msfiles = isa["data.filenames"][[i]][[ isatab.syntax$raw.spectral.data.file ]]
+
+    pd = try(read.AnnotatedDataFrame(file.path(isa["path"], isa["assay.filenames"][i]),
+                                     row.names = NULL, blank.lines.skip = TRUE, fill = TRUE,
+                                     varMetadata.char = "$", quote="\""))
+
+    sampleNames(pd) = pd$Raw.Spectral.Data.File
 
-    if (isa["assay.filenames"][[i]]==assay.filename){
+    if (length(grep(isatab.syntax$factor.value, colnames(isa["assay.files"][[i]]))) != 0) {
+      ## If there are explicit factors, use them
+      sclass = isa["assay.files"][[i]][ which(isa["assay.files"][[i]][[isatab.syntax$sample.name]] %in% pd$Sample.Name), grep(isatab.syntax$factor.value, colnames(isa["assay.files"][[i]]))[1]]
 
-      if (isatab.syntax$raw.spectral.data.file %in% colnames(isa["data.filenames"][[i]]))
-      {
-        #mass spectrometry files
-        msfiles = isa["data.filenames"][[i]][[ isatab.syntax$raw.spectral.data.file ]]
-
-        pd = try(read.AnnotatedDataFrame(file.path(isa["path"], isa["assay.filenames"][i]),
-                                         row.names = NULL, blank.lines.skip = TRUE, fill = TRUE,
-                                         varMetadata.char = "$", quote="\""))
-
-        sampleNames(pd) = pd$Raw.Spectral.Data.File
-
-        if (length(grep("Factor.Value", colnames(isa["assay.files"][[i]]))) != 0) {
-          ## If there are explicit factors, use them
-          sclass = isa["assay.files"][[i]][ which(isa["assay.files"][[i]][[isatab.syntax$sample.name]] %in% pd$Sample.Name), grep("Factor.Value", colnames(isa["assay.files"][[i]]))[1]]
-
-          wd <- getwd()
-          setwd(isa["path"])
-          xset = xcmsSet(files=msfiles, sclass=sclass, ...)
-          setwd(wd)
-        } else {
-          wd <- getwd()
-          setwd(isa["path"])
-          ## Otherwise just use what was there
-          xset = try(xcmsSet(msfiles, phenoData=pData(pd), ...))
-          setwd(wd)
-        }
-        return(xset)
-      }#if
+      wd <- getwd()
+      setwd(isa["path"])
+      xset = xcmsSet(files=msfiles, sclass=sclass, ...)
+      setwd(wd)
 
-    }#if 
-  }#for
+    } else {
+      wd <- getwd()
+      setwd(isa["path"])
+      ## Otherwise just use what was there
+      xset = try(xcmsSet(msfiles, phenoData=pData(pd), ...))
+      setwd(wd)
+    }
+    return(xset)
+  }#if
+
 }#processAssayXcmsSet
 
 
@@ -50,41 +48,39 @@ processAssayXcmsSet = function(isa, assay.filename, ...){
 
   phenodata.data.frame <- as.data.frame(isa["factors"])
 
+  assay.names <- isa["assay.names"][assay.filename]
 
+  row.names(phenodata.data.frame) <- assay.names[[assay.filename]][[1]]
 
-  for(i in seq_len(length(isa["assay.filenames"]))){
+  i <- which(isa["assay.filenames"]==assay.filename)
+
+  if (isatab.syntax$raw.spectral.data.file %in% colnames(isa["data.filenames"][[i]]))
+  {
+    #mass spectrometry files
+    msfiles = isa["data.filenames"][[i]][[ isatab.syntax$raw.spectral.data.file ]]
+
+    pd = try(read.AnnotatedDataFrame(file.path(isa["path"], isa["assay.filenames"][i]),
+                                     row.names = NULL, blank.lines.skip = TRUE, fill = TRUE,
+                                     varMetadata.char = "$", quote="\""))
+
+    sampleNames(pd) = pd$Raw.Spectral.Data.File
 
-    if (isa["assay.filenames"][[i]]==assay.filename){
+    if (length(grep(isatab.syntax$factor.value, colnames(isa["assay.files"][[i]]))) != 0) {
+      ## If there are explicit factors, use them
+      sclass = isa["assay.files"][[i]][ which(isa["assay.files"][[i]][[isatab.syntax$sample.name]] %in% pd$Sample.Name), grep(isatab.syntax$factor.value, colnames(isa["assay.files"][[i]]))[1]]
 
-      if (isatab.syntax$raw.spectral.data.file %in% colnames(isa["data.filenames"][[i]]))
-      {
-        #mass spectrometry files
-        msfiles = isa["data.filenames"][[i]][[ isatab.syntax$raw.spectral.data.file ]]
-
-        pd = try(read.AnnotatedDataFrame(file.path(isa["path"], isa["assay.filenames"][i]),
-                                         row.names = NULL, blank.lines.skip = TRUE, fill = TRUE,
-                                         varMetadata.char = "$", quote="\""))
-
-        sampleNames(pd) = pd$Raw.Spectral.Data.File
-
-        if (length(grep("Factor.Value", colnames(isa["assay.files"][[i]]))) != 0) {
-          ## If there are explicit factors, use them
-          sclass = isa["assay.files"][[i]][ which(isa["assay.files"][[i]][[isatab.syntax$sample.name]] %in% pd$Sample.Name), grep("Factor.Value", colnames(isa["assay.files"][[i]]))[1]]
-
-          wd <- getwd()
-          setwd(isa["path"])
-          xset = xcmsSet(files=msfiles, sclass=sclass, ...)
-          setwd(wd)
-        } else {
-          wd <- getwd()
-          setwd(isa["path"])
-          ## Otherwise just use what was there
-          xset = try(xcmsSet(msfiles, phenoData=pData(pd), ...))
-          setwd(wd)
-        }
-        return(xset)
-      }#if
+      wd <- getwd()
+      setwd(isa["path"])
+      xset = xcmsSet(files=msfiles, sclass=sclass, ...)
+      setwd(wd)
 
-    }#if 
-  }#for
+    } else {
+      wd <- getwd()
+      setwd(isa["path"])
+      ## Otherwise just use what was there
+      xset = try(xcmsSet(msfiles, phenoData=pData(pd), ...))
+      setwd(wd)
+    }
+    return(xset)
+  }#if
 }#processAssayXcmsSet

R/Risa.R

@@ -17,6 +17,7 @@ isatab.syntax <- list(
   array.data.file="Array Data File",
   raw.spectral.data.file="Raw Spectral Data File",
   factor.name="Factor Name",
+  factor.value="Factor Value",
   assay.name="Assay Name"
   )