## ----------------------------------------------------------------------------- library(SCANVIS) data(SCANVISexamples) names(gen19) ## ----------------------------------------------------------------------------- head(gbm3) gbm3.scn<-SCANVISscan(sj=gbm3,gen=gen19,Rcut=5,bam=NULL,samtools=NULL) head(gbm3.scn) ## ----------------------------------------------------------------------------- head(gbm3.vcf) gbm3.scnv<-SCANVISlinkvar(gbm3.scn,gbm3.vcf,gen19) gbm3.scnv[10:23,] ## ----------------------------------------------------------------------------- gbm3.scnv[38:51,] ## ----------------------------------------------------------------------------- gbm3.scnvp<-SCANVISlinkvar(gbm3.scn,gbm3.vcf,gen19,p=100) table(gbm3.scnv[,'passedMUT']) table(gbm3.scnvp[,'passedMUT']) ## ----------------------------------------------------------------------------- par(mfrow=c(2,1),mar=c(1,1,1,1)) vis.lusc1<-SCANVISvisual('PPA2',gen19,LUSC[[1]],TITLE=names(LUSC)[1],full.annot=TRUE,bam=NULL,samtools=NULL) vis.lusc2<-SCANVISvisual('PPA2',gen19,LUSC[[2]],TITLE=names(LUSC)[2],full.annot=TRUE,bam=NULL,samtools=NULL,USJ='RRS') ## ----------------------------------------------------------------------------- ASJ<-tail(vis.lusc2[[2]])[,1:3] c2<-SCANVISvisual('PPA2',gen19,LUSC[[2]],TITLE=names(LUSC)[2],full.annot=TRUE,SJ.special=ASJ) ## ----------------------------------------------------------------------------- vis.lusc.merged<-SCANVISvisual('PPA2',gen19,LUSC,TITLE='Two LUSC samples, merged',full.annot=TRUE) ## ----------------------------------------------------------------------------- sessionInfo()