track_clones: Identifies or tracks integration sites through multiple...

In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description

Given a GRangesList of integration site sets, this function will return a GRangesList (separated by position ID) of all sites shared within the gap distance between the sets. Using the track.origin option (default = TRUE) will append a column to the metadata of the GRanges objects designating which set they originated in. If the GRangesList has names, these designations will be the names of the list items. Note: as the output is a GRangesList separated by position ID, some list objects may appear to come only from one origin set, but they will overlap within the gap distance to another list object from a different origin.

Usage

track_clones(sites.list)

track_clones(sites.list, gap = 5L, track.origin = TRUE)

Arguments

sites.list	a GRangesList object containing sets of integration sites or ranges (one per row).
gap	an integer designating the nucleotide distance or window for which to group integration sites.
track.origin	logical for whether to append information regarding the origin of the integration site. Use if there is no sample information in the metadata columns of the input GRanges objects.
quiet	logical for whether or not to message to the terminal processing findings. True by default.

Details

track_clones returns a GRangesList of integration sites shared between multiple GRanges objects.

Author(s)

Christopher Nobles, Ph.D.

Examples

gr <- GRanges(
  seqnames = rep("chr1", 100),
  ranges = IRanges(
    start = 1:100,
    width = sample(30:100, 100, replace = TRUE)),
  strand = rep(c("+", "-"), 50))

gr1 <- sample(gr, 50)
gr2 <- sample(gr, 50)

grl <- GRangesList(gr1, gr2)

track_clones(grl, gap = 0L, track.origin = TRUE)

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