Removed exclusive references to the RPKM normalisation method from do…

…cs + changed the name of the slot 'rpkm' to 'texp'

tviz/NAMESPACE

@@ -3,7 +3,7 @@ exportClasses( "TranscriptExpressionSet" )
 exportMethods(
    id,
    conditions,
-   rpkms,
+   texp,
    gexp,
    dominance,
    biotypes,

tviz/R/AllClasses.R

@@ -1,7 +1,7 @@
 setClass("TranscriptExpressionSet",
   representation = representation(
     id="character",
-    rpkms="matrix",
+    texp="matrix",
     conditions="list",
     gexp="numeric",
     dominance="numeric",

tviz/R/AllGenerics.R

@@ -8,8 +8,8 @@ setGeneric("id",
 setGeneric("conditions", 
 	function(object) standardGeneric("conditions"))
 
-setGeneric("rpkms", 
-	function(object) standardGeneric("rpkms"))
+setGeneric("texp", 
+	function(object) standardGeneric("texp"))
 
 setGeneric("gexp", 
 	function(object) standardGeneric("gexp"))

tviz/R/functions.R

@@ -7,14 +7,14 @@ readExpressionData=function(gId=gId, infile=infile, cond1=cond1, cond2=cond2) {
   cond1=.format_cond(cond1)
   cond2=.format_cond(cond2)
 
-  # transcript RPKMs
+  # transcript expression levels
   command=paste("grep", gId, infile, sep=" ")
   data=read.table(pipe(command), col.names=header,
     colClasses=c("NULL", "character", rep("numeric", length(header)-2)))
-  rpkms=as.matrix(data[,c(cond1, cond2)])
-  rownames(rpkms)=data[,1]
+  texp=as.matrix(data[,c(cond1, cond2)])
+  rownames(texp)=data[,1]
 
-  return(rpkms)
+  return(texp)
 }
 
 readBiotypeData=function(gId=gId, infile=infile) {
@@ -40,20 +40,20 @@ readSignificantEvents=function(gId=gId, infile=infile) {
   return(significant_events)
 }
 
-newTranscriptExpressionSet=function(gId=gId, rpkms=rpkms, biotypes=biotypes, significant_events=significant_events, cond1=cond1, cond2=cond2) {
+newTranscriptExpressionSet=function(gId=gId, texp=texp, biotypes=biotypes, significant_events=significant_events, cond1=cond1, cond2=cond2) {
   # conditions
   cond1=.format_cond(cond1)
   cond2=.format_cond(cond2)
 
   cond1=cond1-1
-  cond2=seq(from=length(cond1)+1, to=dim(rpkms)[2], by=1)
+  cond2=seq(from=length(cond1)+1, to=dim(texp)[2], by=1)
   conditions=list(cond1=cond1, cond2=cond2)
 
   # create TranscriptExpressionSet object
   tes=new("TranscriptExpressionSet",
     id=gId,
     conditions=conditions,
-    rpkms=rpkms,
+    texp=texp,
     biotypes=biotypes,
     significant_events=significant_events
   )

tviz/R/methods-TranscriptExpressionSet.R

@@ -1,10 +1,10 @@
 ## initialize
 setMethod("initialize", "TranscriptExpressionSet",
-  function(.Object, id=id, rpkms=rpkms, biotypes=biotypes, conditions=conditions, significant_events=significant_events){
+  function(.Object, id=id, texp=texp, biotypes=biotypes, conditions=conditions, significant_events=significant_events){
     .Object@id=id
-    .Object@rpkms=rpkms
+    .Object@texp=texp
     .Object@conditions=conditions
-    .Object@gexp=colSums(.Object@rpkms)
+    .Object@gexp=colSums(.Object@texp)
     .Object@dominance=.calculate_dominance(.Object)
     .Object@.relexp=.calculate_relexp(.Object)
     .Object@.scaledexp=.calculate_scaledexp(.Object)
@@ -20,9 +20,9 @@ setMethod("show",
   function(object) {
     cat("Object of class",class(object),"\n")
     cat("   Id:",id(object),"\n")
-    cat("   RPKMs: data frame with", dim(object@rpkms)[1], "transcripts and", dim(object@rpkms)[2], "samples\n")
-    cat("     transcripts:", head(rownames(object@rpkms), n=4), "(...)\n")
-    cat("     samples:", head(colnames(object@rpkms), n=4), "(...)\n")
+    cat("   Transcript expression: data frame with", dim(object@texp)[1], "transcripts and", dim(object@texp)[2], "samples\n")
+    cat("     transcripts:", head(rownames(object@texp), n=4), "(...)\n")
+    cat("     samples:", head(colnames(object@texp), n=4), "(...)\n")
     cat("   Conditions:\n")
     cat("     condition 1:", head(object@conditions$cond1, n=4), "(...)\n")
     cat("     condition 2:", head(object@conditions$cond2, n=4), "(...)\n")
@@ -44,8 +44,8 @@ setMethod("id", "TranscriptExpressionSet", function(object) object@id)
 setMethod("conditions", "TranscriptExpressionSet", 
   function(object) object@conditions)
 
-setMethod("rpkms", "TranscriptExpressionSet", 
-  function(object) object@rpkms)
+setMethod("texp", "TranscriptExpressionSet", 
+  function(object) object@texp)
 
 setMethod("gexp", "TranscriptExpressionSet", 
   function(object) object@gexp)
@@ -202,7 +202,7 @@ setMethod(".plot_boxplots",
       .subplot_boxplots(
         ldata=list(tes@gexp[tes@conditions$cond1], tes@gexp[tes@conditions$cond2]),
         xlab=tes@id, 
-        ylab="gene expression (RPKMs)", 
+        ylab="gene expression", 
         type="gexp", 
         mar=mar, 
         col=col, 
@@ -328,7 +328,7 @@ setMethod(".plot_segments",
         data1=tes@gexp[tes@conditions$cond1], 
         data2=tes@gexp[tes@conditions$cond2], 
         xlab=tes@id, 
-        ylab="gene expression (RPKMs)", 
+        ylab="gene expression", 
         type="gexp", 
         mar=mar, 
         col=col, 
@@ -446,7 +446,7 @@ setMethod(".get_legend_title_starplot", "TranscriptExpressionSet",
   function(object) {
     legend_title=paste(
       object@id, "\n\n",
-      "gene expression summary (RPKMs):\n", 
+      "gene expression summary:\n", 
       "   condition 1 (left) - ", .distr_summary(object@gexp[object@conditions$cond1]), "\n",
       "   condition 2 (right) - ", .distr_summary(object@gexp[object@conditions$cond2]), "\n\n",
       "dominance summary:\n",
@@ -459,13 +459,13 @@ setMethod(".get_legend_title_starplot", "TranscriptExpressionSet",
 
 setMethod(".calculate_dominance", "TranscriptExpressionSet",
     function(object) {
-          dominance=apply(object@rpkms, 2, .ratio_second)
+          dominance=apply(object@texp, 2, .ratio_second)
           return(dominance)
     })
 
 setMethod(".calculate_relexp", "TranscriptExpressionSet",
     function(object) {
-      relexp=t(t(object@rpkms)/object@gexp)
+      relexp=t(t(object@texp)/object@gexp)
       return(relexp)
     })
 

tviz/inst/tests/test-tviz.R

@@ -19,7 +19,7 @@ outdir='./output-test'
 dir.create(outdir, showWarnings = FALSE)
 
 ## load data
-rpkms=readExpressionData(gId=gId, infile=expdata, cond1=cond1, cond2=cond2)
+texp=readExpressionData(gId=gId, infile=expdata, cond1=cond1, cond2=cond2)
 biotypes=readBiotypeData(gId=gId, infile=annot)
 if (filt != "NA") {
 	significant_events=readSignificantEvents(gId=gId, infile=filt)
@@ -30,7 +30,7 @@ if (filt != "NA") {
 ## create TranscriptExpressionSet object
 tes=newTranscriptExpressionSet(
         gId=gId,
-        rpkms=rpkms,
+        texp=texp,
         biotypes=biotypes,
         cond1=cond1,
         cond2=cond2,
@@ -61,7 +61,7 @@ outdir='./output-test'
 dir.create(outdir, showWarnings = FALSE)
 
 ## load data
-rpkms=readExpressionData(gId=gId, infile=expdata, cond1=cond1, cond2=cond2)
+texp=readExpressionData(gId=gId, infile=expdata, cond1=cond1, cond2=cond2)
 biotypes=readBiotypeData(gId=gId, infile=annot)
 if (filt != "NA") {
 	significant_events=readSignificantEvents(gId=gId, infile=filt)
@@ -72,7 +72,7 @@ if (filt != "NA") {
 ## create TranscriptExpressionSet object
 tes=newTranscriptExpressionSet(
         gId=gId,
-        rpkms=rpkms,
+        texp=texp,
         biotypes=biotypes,
         cond1=cond1,
         cond2=cond2,

tviz/man/TranscriptExpressionSet-class.Rd

@@ -11,7 +11,7 @@
 \section{Slots}{
   \describe{
   \item{gId}{Id for the gene to be plotted.}
-  \item{rpkms}{Matrix of transcript RPKM/FPKM values in each sample, 
+  \item{texp}{Matrix of transcript expression values in each sample, 
   loaded using the 'readExpressionData' function.}
   \item{biotypes}{Matrix of biotypes for each of the annotated transcripts within the gene, 
   loaded using the 'readBiotypeData' function.}

tviz/man/newTranscriptExpressionSet.Rd

@@ -9,15 +9,15 @@ embedded expression data.}
 \usage{
 newTranscriptExpressionSet( 
   gId=gId, 
-  rpkms=rpkms, 
+  texp=texp, 
   biotypes=biotypes, 
   significant_events=significant_events, 
   cond1=cond1, 
   cond2=cond2)
 }
 \arguments{
   \item{gId}{Id for the gene to be plotted.}
-  \item{rpkms}{Matrix of transcript RPKM/FPKM values in each sample, 
+  \item{texp}{Matrix of transcript expression values in each sample, 
   loaded using the 'readExpressionData' function.}
   \item{biotypes}{Matrix of biotypes for each of the annotated transcripts within the gene, 
   loaded using the 'readBiotypeData' function.}

tviz/man/plotDistr.Rd

@@ -8,7 +8,7 @@
 \description{
 A distribution plot contains information on the distribution of gene expression levels, major transcript dominance and transcript relative abundances in each condition. This plot contains three panels:
 
-left - Distribution of gene expression levels (RPKMs or FPKMs).
+left - Distribution of gene expression levels.
 
 middle - Distribution of major transcript dominance. Major transcript dominance is calculated in each condition as the ratio of expression of the second v.s. first most abundant transcripts. Thus, a ratio close to 0 will indicate that the most abundant transcript is dominating the expression for that gene, while a ratio close to 1 indicates that the first and second most abundant transcripts are expressed at the same level.
 

tviz/man/plotStars.Rd

@@ -6,7 +6,7 @@
 \title{Create a starplot for the specified TranscriptExpressionSet object.}
 
 \description{
-A starplot provides information on the transcript RPKM quantifications in a sample specific manner.
+A starplot provides information on the transcript quantifications in a sample specific manner.
 In this plot each sample is represented as a pie chart, where each of the slices corresponds to a transcript. The size of each slice is proportional to the transcript expression level, and the overall size of the plot is proportional to the gene expression level, thus allowing comparisons across samples.
 }
 

tviz/man/readExpressionData.Rd

@@ -5,10 +5,10 @@
 \alias{readExpressionData}
 
 \title{
-   Create a matrix of RPKM/FPKM transcript expression levels for a given gene from the specified input file.
+   Create a matrix of transcript expression levels for a given gene from the specified input file.
 }
 \description{
-   Loads transcript expression data (RPKM/FPKM values) for a given gene from the specified input file. 
+   Loads transcript expression data for a given gene from the specified input file. 
    Each sample is represented as a column, and each transcript as a row.
 }
 \usage{

tviz/man/rpkms.Rd → tviz/man/texp.Rd

@@ -1,19 +1,19 @@
-\name{rpkms}
+\name{texp}
 \encoding{UTF-8}
 \Rdversion{1.1}
 \docType{methods}
-\alias{rpkms,TranscriptExpressionSet-method}
-\alias{rpkms}
+\alias{texp,TranscriptExpressionSet-method}
+\alias{texp}
 \title{
-   Accessor function for the 'rpkms' slot of a TranscriptExpressionSet object.
+   Accessor function for the 'texp' slot of a TranscriptExpressionSet object.
 }
 
 \description{
-   The rpkms slot displays a matrix with the initial RPKM/FPKM values provided by the user. Each sample is represented as a column, and each transcript as a row.
+   The texp slot displays a matrix with the initial expression values provided by the user. Each sample is represented as a column, and each transcript as a row.
 }
 
 \usage{
-\S4method{rpkms}{TranscriptExpressionSet}(object)
+\S4method{texp}{TranscriptExpressionSet}(object)
 }
 
 \arguments{