fiveTo3List: Reorders each rearrangement as two 5-prime to 3-prime...
In cancer-genomics/trellis: Somatic structural variant analysis

fiveTo3List

R Documentation

Reorders each rearrangement as two 5-prime to 3-prime orientations

Description

Reorders each rearrangement as two 5-prime to 3-prime orientations

Usage

fiveTo3List(rlist, build)

Arguments

`rlist`	a `RearrangementList`
`build`	character string providing genome build (only hg19 or hg18 are supported)

Value

a RearrangementList

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")
 ## Not run: 
   rlist2 <- fiveTo3List(rlist[near.coding], build="hg19")
   rlist2

## End(Not run)

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