fmain: Run HSA

In HenrikBengtsson/hsa: Integrating Multi-Track Hi-C Data for Genome-Scale Reconstruction of 3D Chromatin Structure (a Non-Official R Package)

Description

This fmain() function is an tidied-up and packaged version of the one available in the R scripts provided by Zuo et al. (2016) available from the authors' website http://ouyanglab.jax.org/hsa/. For details on usage, please see the instructions provided by the authors at their website.

Usage

fmain(lsmap0, lscov0, outfile, Maxiter, submaxiter, lambda, Leapfrog, epslon,
  mkfix = 0, rho = 0, mk, initialS = NULL, coarsefit = TRUE,
  rmoutlier = FALSE, fitmode = 0)

Arguments

lsmap0	To be documented.
lscov0	To be documented.
outfile	To be documented.
Maxiter	To be documented.
submaxiter	To be documented.
lambda	To be documented.
Leapfrog	To be documented.
epslon	To be documented.
mkfix	To be documented.
rho	To be documented.
mk	To be documented.
initialS	To be documented.
coarsefit	To be documented.
rmoutlier	To be documented.
fitmode	To be documented.

Value

A named list with elements Ao, bo, invSigmao, Po, and betao.

References

Zou C, Zhang Y, Ouyang Z. (2016) HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure. Genome Biology, 17:40. PMC4774023

See Also

http://ouyanglab.jax.org/hsa/

HenrikBengtsson/hsa documentation built on July 6, 2019, 2:13 a.m.