SCANVISreadSTAR: upload SJ.tab STAR file in SCANVISuse

In nygenome/SCANVIS: SCANVIS - a tool for SCoring, ANnotating and VISualizing splice junctions

Description

This function is a little wrapper for reading in splice junction details from the SJ.tab file output by the STAR alignment tool.

Usage

SCANVISread_STAR(sj_file)

Arguments

sj_file

url to SJ file output by STAR aligner

Value

SJ data in matrix format as required for SCANVISfunctions

Examples

#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

nygenome/SCANVIS documentation built on July 19, 2019, 4:57 a.m.