HiCseg.callTAD: HiCseg.callTAD

In robinweide/GENOVA: GENOVA: expore the Hi-C

HiCseg.callTAD

Description

A wrapper with call TADs with HiCseg of Lévy-Leduc et al. (2018)

Usage

HiCseg.callTAD(
  experiment,
  chromsToUse = NULL,
  binPerBorder = 3,
  chunk = NULL,
  BEDcolor = "255,255,0",
  verbose = F
)

Arguments

experiment	The Hi-C experiment object: produced by construct.experiment().
chromsToUse	The chromosome(s) of interest. Omitting this leads to the computation across all chromosomes.
binPerBorder	Minimum number of bins per border: used to set the maximal number of change-points. The default (3) set this maximal number of borders to nbins/3.
chunk	Use chunks of [chunk]bp instead of the whole arm: the whole arm can be a big burden, so it could be beneficial to use chunks of a set size (e.g. 5e6). But be carefull: the segmentation will be different from the full arm!!!
BEDcolor	Color of items in the resulting BEDPE-file
verbose	Bioinformatics can be a bit lonely: set this to true to get a more chatty function.

Value

A BEDPE-df

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.