rearDataFrame: Create a data.frame of rearranged read pairs and split reads...

In cancer-genomics/trellis: Somatic structural variant analysis

Create a data.frame of rearranged read pairs and split reads supporting a rearrangement

Description

This function is useful for converting a Rearrangement object to a data.frame for subsequent visualization by ggplot.

Usage

rearDataFrame(r, build, maxgap = 5000)

Arguments

r	a Rearrangement object
build	character string indicating genome build (only hg19 and hg18 currently supported)
maxgap	the allowable distance between a split or paired end read and a transcript for assessing whether coding regions

Examples

  extdata <- system.file("extdata", package="svbams")
  rfile <- file.path(extdata, "CGOV11T_1.bam.rds")
  rlist <- readRDS(rfile)
  r <- rlist[[1]]
  r2 <- fiveTo3Prime(r, "hg19")
  rearDataFrame(r2[[1]], "hg19") 

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