segmentOverlaps_bed: calculate segment overlap statistics using UCSC bedtools
In raim/segmenTools: Tools for Functional Genome Exploration

segmentOverlaps_bed

R Documentation

calculate segment overlap statistics using UCSC bedtools

Description

This function produces the same output as segmentOverlaps, but using a command-line call to UCSC bedtools, which must be installed, and starting from normal genome coordinates (w/o indexing; 0-based and inclusive start and end). It temporarily creates bed files, and can require quite a lot of disk space. However, it is faster than segmentOverlaps, and likely better tested.

Usage

segmentOverlaps_bed(
  query,
  target,
  qclass,
  tclass,
  prefix = "cl_",
  chrL,
  perm,
  tmpdir,
  runid,
  overlaps = FALSE,
  symmetric = FALSE,
  save.permutations = FALSE,
  verb = 1
)

Arguments

`query`	query segment table, will be permutated.
`target`	target segment table.
`qclass`	column name which holds a sub-classification (clustering) of the query segments, omit to use all.
`tclass`	column name which holds a sub-classification (clustering) of the target segments, omit to use all.
`prefix`	prefix to be added to the name and score columns of bed files (column 4,5), used to get unique names.
`chrL`	obligatory vector of chromosome length, in the order used as index in the `chr` column of query and target.
`perm`	number of permutations for calculating statistics.
`tmpdir`	temporary directory, useful to provide for debugging, or exploring detailed results.
`runid`	use this ID for the run, for more recognizable jobnames. This is potentially dangerous since each call MUST have a unique name.
`overlaps`	allow overlaps in the permutations of query segments.
`symmetric`	treat test as symmetric. This is only useful for the case where overlaps all segments from the forward strand and the reverse strand are tested, to find antisense overlaps within a segment classification.
`save.permutations`	save permutated query bed files used in p-value calculation. If this is provided together with `tmpdir`, the randomized bed files can be re-used. However, this may be dangerous or cause errors when different queries and targets are used with the same `tmpdir`.
`verb`	verbosity level, 0: silent.