get_contacts: Create a list of information for a set of intervals

In ChristopherBarrington/domainClassifyR: Classification of Hi-C interaction domains

Description

Extracts interaction frequency information for a set of 2D intervals. The domain information is cached for quick loading, or loaded from the cache if the parameters have been run (and cached) before.

Usage

get_contacts(domains,
  track_nm = "hic.Genome_Structure_Development.AST_NS_WT.tracks.observed_new_score",
  band = c(10000, 15000000),
  cache.path = "/home/cbarring/CLASSIFY_DOMAINS.CACHE",
  distribute_method = "PARALLEL", sge.resources = list(h_rt = "00:30:00"),
  max_jobs = 500, cluster_size = 10, get.fends = FALSE)

Arguments

domains	A data.frame of 2D intervals
track_nm	Name of the score track from which fend pairs are extracted
band	Genomic distance between fend pairs to consider
cache.path	Absolute path to the directory that cached domains can be found or saved
distribute_method	Specify where the jobs to define each interval/domain should be distributed (using distributR)
sge.resources, max_jobs, cluster_size	Parameters passed to distributR
get.fends	Extracting the valid fragment ends and identifying potential 2D interactors (uses masses of memory!)

Value

The contacts list, with additional information

See Also

distributR for information on distributed jobs.

ChristopherBarrington/domainClassifyR documentation built on May 3, 2019, 5:22 p.m.