Fixed merge

DESCRIPTION

@@ -1,10 +1,11 @@
 Package: cummeRbund
-Title: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
-Version: 2.9.3
+
+Version: 2.13.1
 Date: 2013-04-22
 Author: L. Goff, C. Trapnell, D. Kelley
 Description: Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data.  In addition, provides numerous plotting functions for commonly used visualizations.
-Imports: methods, plyr, BiocGenerics, Biobase
+Imports: methods, plyr, BiocGenerics, S4Vectors (>= 0.9.25), Biobase
+
 Depends: R (>= 2.7.0), BiocGenerics (>= 0.3.2), RSQLite, ggplot2, reshape2, fastcluster, rtracklayer, Gviz
 Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson
 Maintainer: Loyal A. Goff <[email protected]>

NAMESPACE

@@ -1,9 +1,11 @@
-importFrom(BiocGenerics, annotation)
-
 import(methods)
 
 #importFrom(graphics, plot)
 importFrom(plyr, defaults)
+
+importFrom(BiocGenerics, annotation)
+import(S4Vectors)
+
 importFrom(Biobase, featureNames)
 
 exportClasses(CuffSet,

R/database-setup.R

@@ -1950,7 +1950,8 @@ readCufflinks<-function(dir = getwd(),
 		stop("Must provide a dbConn connection")
 
 	write("Reading GTF file",stderr())
-	gr<-import(gtfFile,asRangedData=FALSE)
+
+	gr<-import(gtfFile)
 	gr<-as(gr,"data.frame")
 	#gr$genome<-genomebuild
 	colnames(gr)[grepl('^transcript_id$',colnames(gr))]<-'isoform_id'
@@ -1981,7 +1982,11 @@ readCufflinks<-function(dir = getwd(),
 	requiredAttribs <- c("gene_id", "transcript_id", "exon_number")
 
 	if (verbose) message("Importing ", gtfFile)
+<<<<<<< HEAD
 	tmp <- import(gtfFile, asRangedData=FALSE)
+=======
+	tmp <- import(gtfFile)
+>>>>>>> a4a2fc9b30204a4d0b68f44cdbaa7a8b7000efbe
 
 	#dispose of unspliced unstranded transcripts
 	#tmp <- tmp[ which(strand(tmp) %in% c('+','-')) ]
@@ -2014,7 +2019,11 @@ readCufflinks<-function(dir = getwd(),
 	tmpS <- split(tmp, values(tmp)$transcript_id)
 	if(verbose) message('Attempting to create the splicings data.frame')
 	splicings <- data.frame(
+<<<<<<< HEAD
 			tx_id=rep(1:length(tmpS), elementLengths(tmpS)),
+=======
+			tx_id=rep(1:length(tmpS), elementNROWS(tmpS)),
+>>>>>>> a4a2fc9b30204a4d0b68f44cdbaa7a8b7000efbe
 			exon_rank=as.integer(values(unlist(tmpS))$exon_number),
 			exon_chrom=as.character(seqnames(unlist(tmpS))),
 			exon_strand=as.character(strand(unlist(tmpS))),
@@ -2033,7 +2042,11 @@ readCufflinks<-function(dir = getwd(),
 
 	#create the db
 	if (verbose) message("Creating TranscriptDb")
+<<<<<<< HEAD
 	tmpdb <- makeTranscriptDb(transcripts, splicings, genes=genes)
+=======
+	tmpdb <- makeTxDb(transcripts, splicings, genes=genes)
+>>>>>>> a4a2fc9b30204a4d0b68f44cdbaa7a8b7000efbe
 	if (verbose) message("Use saveFeatures() to save the database to a file")
 	return(tmpdb)
 

R/methods-CuffData.R

@@ -776,7 +776,8 @@ setMethod("csVolcano",signature(object="CuffData"), .volcano)
 
 	p <-ggplot(dat) + geom_point(mapping,na.rm=TRUE,size=0.8) + scale_colour_manual(values = c("black","red")) + facet_grid(sample_1~sample_2)
 
-	p<- p + geom_vline(aes(x=0),linetype=2)
+	p<- p + geom_vline(aes(xintercept=0),linetype=2)
+
 
 	p <- p + theme_bw() + xlab(bquote(paste(log[2],"(fold change)",sep=""))) + ylab(bquote(paste(-log[10],"(p value)",sep="")))
 
@@ -961,7 +962,9 @@ setMethod("MDSplot",signature(object="CuffData"),.MDSplot)
 	if(showPoints){
 		plot<- plot + geom_point(alpha=.4, size=0.8, aes(label=obsnames))
 	}
-	plot <- plot + geom_hline(aes(0), size=.2) + geom_vline(aes(0), size=.2) #+ geom_text(aes(label=shoutout),size=2,color="red")
+
+	plot <- plot + geom_hline(aes(yintercept=0), size=.2) + geom_vline(aes(xintercept=0), size=.2) #+ geom_text(aes(label=shoutout),size=2,color="red")
+
 	datapc <- data.frame(varnames=rownames(PC$rotation), PC$rotation)
 	mult <- min(
 			(max(dat[,y]) - min(dat[,y])/(max(datapc[,y])-min(datapc[,y]))),

R/methods-CuffFeatureSet.R

@@ -1146,7 +1146,9 @@ setMethod("MDSplot",signature(object="CuffFeatureSet"),.MDSplot)
 	if(showPoints){
 		plot<- plot + geom_point(alpha=.4, size=0.8, aes(label=obsnames))
 	}
-	plot <- plot + geom_hline(aes(0), size=.2) + geom_vline(aes(0), size=.2) #+ geom_text(aes(label=shoutout),size=2,color="red")
+
+	plot <- plot + geom_hline(aes(yintercept=0), size=.2) + geom_vline(aes(xintercept=0), size=.2) #+ geom_text(aes(label=shoutout),size=2,color="red")
+
 	datapc <- data.frame(varnames=rownames(PC$rotation), PC$rotation)
 	mult <- min(
 			(max(dat[,y]) - min(dat[,y])/(max(datapc[,y])-min(datapc[,y]))),

R/methods-CuffGene.R

@@ -171,8 +171,9 @@ setMethod("genePlot",signature(object="CuffGene"),.plot)
 	#print(dat)
 	p<-ggplot(dat,aes(x="",y=fpkm,fill=tracking_id))
 
-	p<- p + geom_bar(stat="identity",position="fill",line="black")
-
+
+	p<- p + geom_bar(stat="identity",position="fill",color="black")
+
 	p<- p + coord_polar(theta='y')
 
 	p<-p + scale_fill_hue(l=50,h.start=200) + scale_color_hue(l=50,h.start=200) + theme_bw()

R/methods-CuffSet.R

@@ -764,11 +764,13 @@ setMethod("getSig",signature(object="CuffSet"),.getSig)
 	sig$testResult<-0
 	sig$testResult[sig$q_value<=alpha]<-1
 
-	fieldsNeeded<-c('gene_id','testName','testResult')
+
+	fieldsNeeded<-c(slot(object,level)@idField,'testName','testResult')
 	sig<-sig[,fieldsNeeded]
 
 	#recast
-	sig.table<-acast(sig,gene_id~testName,value='testResult')
+	sig.table<-acast(sig,as.formula(paste(slot(object,level)@idField,"~testName")),value='testResult')
+
 
 	#remove genes that do not reject null in any test
 	sig.table<-sig.table[rowSums(sig.table,na.rm=T)>0,]

README

@@ -14,10 +14,11 @@ Authors:
 Maintainer:
 	- Loyal A. Goff <[email protected]>
 
+
 Creative Contributions & Support:
 	- John L. Rinn (2)
 	- Manolis Kellis (1)
-	- Ron Hart (3)
+	- Ron Hart (3)	
 	- David Hendrickson (2)
 
 Affiliations: