parseJaccard: parses overlap statitics produced with bedtools

In raim/segmenTools: Tools for Functional Genome Exploration

parses overlap statitics produced with bedtools

Description

Parses a file that is produced by the script segmentoverlaps.sh (based on USCS bedtools), into an clusterOverlaps class.

Usage

parseJaccard(
  ovfile,
  prefix,
  qclass = "query",
  tclass = "target",
  symmetric = FALSE
)

Arguments

ovfile	output file produced by segmentoverlaps.sh.
prefix	prefix to be added to the name and score columns of bed files (column 4,5) to get unique names.
qclass	optional name for the query classes.
tclass	optional name for the target classes.
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.

raim/segmenTools documentation built on May 5, 2024, 11:30 a.m.