serial_cluster: Generate clusterIDs for integration sites given multiple gap...

In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description

Given a GRanges object, this function identifies groups or clusters of integration sites within specified distances. The output is of the same length and order of the input, and clusterID information is appended to the metadata columns.

Usage

serial_cluster(sites, gaps = c(0L, 1L, 2L))

Arguments

sites	a GRanges object where each row is a different integration site or range.
gaps	an integer vector of any length specifying the nucleotide distance allowable between sites to call in the same group or cluster.

Details

serial_cluster returns a GRanges object of the same length and order as input with additional metadata columns specifying the group or clusterID of given nt windows.

Author(s)

Christopher Nobles, Ph.D.

Examples

sites <- GRanges(
  seqnames = rep("chr1", 7),
  ranges = IRanges(
    start = c(50, 49, 44, 50, 50, 50, 60),
    width = seq(20, 26, 1)),
  strand = rep("+", 7))

serial_cluster(sites, gaps = c(1L, 5L, 10L))

cnobles/gintools documentation built on Aug. 22, 2019, 10:36 a.m.