seqJunctionNearTx: Evaluates whether sequence junction of a rearrangement is...
In cancer-genomics/trellis: Somatic structural variant analysis

seqJunctionNearTx

R Documentation

Evaluates whether sequence junction of a rearrangement is within 5000bp of a transcript

Description

Only rearrangements where both sides of the sequence junction are near a transcript are evaluated as candidate in-frame fusions.

Usage

seqJunctionNearTx(rlist, build, maxgap = 5000)

Arguments

`rlist`	a `RearrangementList`
`build`	genome build
`maxgap`	integer for number of basepairs allowed between a candidate sequence junction and the improperly paired read alignments

Value

a logical vector of the same length as the rlist object

Examples

 extdata <- system.file("extdata", package="svbams")
 rfile <- file.path(extdata, "CGOV11T_1.bam.rds")
 rlist <- readRDS(rfile)
 head(seqJunctionNearTx(rlist, "hg19"))

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.