### R code from vignette source 'vignettes/chimera/inst/doc/chimera.Rnw' ################################################### ### code chunk number 1: chimera.Rnw:50-51 ################################################### dir(paste(find.package(package="chimera"),"/examples/", sep="")) ################################################### ### code chunk number 2: chimera.Rnw:85-102 ################################################### #creating a fusion report from output of fusionMap library(chimera) tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"), "/examples/mcf7.FMFusionReport", sep=""), org="hs") #extracting the fSet object for one of the fusions myset <- tmp[[13]] #constructing the fused sequence(s) trs <- chimeraSeqs(myset, type="transcripts") #adding the sequences to the fSet object myset <- addRNA(myset , trs) #extracting sequences from an fSet object tmp.seq <- fusionRNA(myset) #adding reads mapped on the fusion generated using tophatRun function myset <- addGA(myset, paste(path.package(package="chimera"), "/examples/mcf7_trs_accepted_hits.bam",sep="")) #extracting the GAlignments from an fSet object ga <- fusionGA(myset) ################################################### ### code chunk number 3: chimera.Rnw:109-111 ################################################### supporting.reads <- supportingReads(tmp, fusion.reads="encompassing") supporting.reads ################################################### ### code chunk number 4: chimera.Rnw:115-117 ################################################### fusion.names <- fusionName(tmp) fusion.names ################################################### ### code chunk number 5: chimera.Rnw:121-123 ################################################### myset <- tmp[[13]] trs <- chimeraSeqs(myset, type="transcripts") ################################################### ### code chunk number 6: chimera.Rnw:131-140 ################################################### #the DNAStringSet of transcript fusions sequences is saved as fast file #write.XStringSet(trs, paste("SULF2_ARFGEF2.fa",sep=""), format="fasta") if (require(Rsubread)) { subreadRun(ebwt=paste(find.package(package="chimera"),"/examples/SULF2_ARFGEF2.fa",sep=""), input1=paste(find.package(package="chimera"),"/examples/mcf7_sample_1.fq",sep=""), input2=paste(find.package(package="chimera"),"/examples/mcf7_sample_2.fq",sep=""), outfile.prefix="accepted_hits", alignment="se", cores=1) } ################################################### ### code chunk number 7: chimera.Rnw:145-150 ################################################### tmp1 <- filterList(tmp, type="fusion.names", fusion.names[c(1,3,7)]) tmp2 <- filterList(tmp, type="spanning.reads", 2) #tmp3 <- filterList(tmp, type="intronic") tmp4 <- filterList(tmp, type="annotated.genes") tmp5 <- filterList(tmp, type="read.through") ################################################### ### code chunk number 8: chimera.Rnw:156-178 ################################################### tmp <- importFusionData("fusionmap", paste(find.package(package="chimera"), "/examples/mcf7.FMFusionReport", sep=""), org="hs") fusion.names <- fusionName(tmp) myset <- tmp[[13]] trs <- chimeraSeqs(myset, type="transcripts") myset <- addRNA(myset , trs) tmp.seq <- fusionRNA(myset) myset <- addGA(myset, paste(path.package(package="chimera"), "/examples/mcf7_trs_accepted_hits.bam",sep="")) pdf("coverage1.pdf") plotCoverage(myset, plot.type="exons", col.box1="red", col.box2="green", ybox.lim=c(-4,-1)) dev.off() pdf("coverage2.pdf") plotCoverage(myset, plot.type="junctions", col.box1="red", col.box2="yellow", ybox.lim=c(-4,-1)) dev.off() pdf("coverage3.pdf") plotCoverage(myset, junction.spanning=100, fusion.only=TRUE, col.box1="red", col.box2="yellow", ybox.lim=c(-4,-1)) dev.off() ################################################### ### code chunk number 9: chimera.Rnw:207-209 ################################################### mypeps <- fusionPeptides(chimeraSeq.output=trs) mypeps ################################################### ### code chunk number 10: chimera.Rnw:342-346 ################################################### library(xtable) tp <- read.table(paste(find.package(package="chimera"),"/examples/edgren.stat.detection.txt",sep=""), sep="\t", header=T) my.table <- xtable(tp, caption = 'Edgren validated fusions discovered by tools supported by chimera') print(my.table) ################################################### ### code chunk number 11: chimera.Rnw:360-361 ################################################### sessionInfo()