recurrentDeletions: Aggregate deletions to the gene-level when evaluating...
In cancer-genomics/trellis: Somatic structural variant analysis

recurrentDeletions

R Documentation

Aggregate deletions to the gene-level when evaluating recurrence

Description

Aggregate deletions to the gene-level when evaluating recurrence

Usage

recurrentDeletions(tx, grl, maxgap = 5000)

Arguments

`tx`	a `GRanges` object of transcripts
`grl`	a `GRangesList` of deletions – each element is a sample
`maxgap`	length-one integer vector passed to `findOverlaps`

Examples

  genes <- GRanges("chr1", IRanges(5, 10))
  genes$gene_name <- "a"
  gr1 <- GRanges(rep("chr1", 2), IRanges(c(4, 8), c(6, 10)), id=rep("id1", 2))
  gr2 <- GRanges("chr1", IRanges(3, 9), id="id2")
  grl <- GRangesList(id1=gr1, id2=gr2)
  recurrentDeletions(genes, grl, maxgap=5)

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