fiveTo3Prime: Put the linked genomic intervals in 5-prime to 3-prime order...
In cancer-genomics/trellis: Somatic structural variant analysis

fiveTo3Prime

R Documentation

Put the linked genomic intervals in 5-prime to 3-prime order with respect to the rearranged genome

Description

Put the linked genomic intervals in 5-prime to 3-prime order with respect to the rearranged genome

Usage

fiveTo3Prime(r, build, maxgap = 5000)

Arguments

`r`	a `Rearrangement` object
`build`	string providing build of reference genome ('hg18', 'hg19', or 'hg38')
`maxgap`	maximum distance between read and transcript for transcript to be considered overlapping

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")
  df <- rearDataFrame(r2[[1]], "hg19")
  ggRearrange(df)

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