create_net2plot: Create an igraph object of the chromatin interaction network...

In LucaGiudice/Esearch3D: Leveraging gene expression and chromatin architecture to predict intergenic enhancers

Description

Given the input and output of the two step network based propagation, it assembles an igraph object of the CIN with all the information included in order to be visualized or analysed

Usage

create_net2plot(
  g_net,
  input_m,
  gf_prop,
  ann_net_b,
  frag_pattern = "F",
  ff_net = NULL,
  ff_prop = NULL
)

Arguments

g_net	Edge list of the chromatin interaction network such that first column are genes and second column are "FragX" fragments
input_m	numeric matrix of a cell expression profile before the propagation
gf_prop	numeric matrix of a cell profile after the first step of the propagation applied with only the gene-genic fragment component of the CIN
ann_net_b	matrix, for each row presents the gene identifier, the chromosome in which the gene is, the starting end ending position in the sequence.
frag_pattern	string, initial character of the fragments name (e.g. "F" or "Frag")
ff_net	Edge list of the chromatin interaction network such that first and second column are "FragX" fragments
ff_prop	numeric matrix of a cell profile after the second step of the propagation applied with the fragment-fragment component of the CIN

Value

igraph object

LucaGiudice/Esearch3D documentation built on Dec. 17, 2021, 1:12 a.m.