SCANVISread_STAR {SCANVIS} | R Documentation |
This function is a little wrapper for reading in splice junction details from the SJ.tab file output by the STAR alignment tool.
SCANVISread_STAR(sj_file)
sj_file |
url to SJ file output by STAR aligner |
SJ data in matrix format as required for SCANVISfunctions
#set up toy example with chr,start,end,strand tmp=cbind(rep('chr1',10),seq(100,1000,100),seq(100,1000,100)+99,rep(2,10)) #add in intron motif, annot, num read, num multimap reads, max overhang #see STAR manual for details tmp=cbind(tmp,rep(2,10),rep(0,10),c(rep(500,5),rep(8,5)),rep(0,10),rep(50,10)) write.table(tmp,'tmp',sep='\t',quote=FALSE,row.names=FALSE,col.names=FALSE) sj=SCANVISread_STAR('tmp') #sj is now suitable as input for SCANVISscan