fiveTo3Prime: Put the linked genomic intervals in 5-prime to 3-prime order...

In cancer-genomics/trellis: Somatic structural variant analysis

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

See Also

rearDataFrame ggRearrange

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 Feb. 2, 2023, 7:04 p.m.