seqJunctions_Rlist: Use split reads for each rearrangement to more precisely...

In cancer-genomics/trellis: Somatic structural variant analysis

Use split reads for each rearrangement to more precisely define sequence boundry

Description

This function constructs a GRanges object of the 5-prime and 3-prime sequence junctions for a RearrangementList that has already been ordered by its two 5-prime to 3-prime orientation.

Usage

seqJunctions_Rlist(rlist)

Arguments

rlist

a RearrangementList

Value

a GRanges object of the 5-prime and 3-prime sequence junctions. The 3-prime junctions are included in the '3p' field of the GRanges object

Examples

 library(trellis)
 extdata <- system.file("extdata", package="svbams")
 rfile <- file.path(extdata, "CGOV11T_1.bam.rds")
 rlist <- readRDS(rfile)
 near.coding <- seqJunctionNearTx(rlist, "hg19")
 ## Just do the first two
 index <- which(near.coding)[1:2]
 rlist2 <- fiveTo3List(rlist[index], build="hg19")
 jxns <- seqJunctions_Rlist(rlist2)
 jxns

cancer-genomics/trellis documentation built on Aug. 20, 2024, 5:48 p.m.