network_analysis: Interaction network topological analysis

Description Arguments Details

View source: R/network_analysis.R

Description

help user plot interaction network picture and make clusters

Arguments

bedFile

the path of specific sites, should use BED format

matrix_dir

the path of matrix, which is output by function generate_matirx()

outputpdf

the picture format of result, if set FALSE, result will be plotted at JPEG format, if TRUE, result will be ploted at PDF format

chrom

which chromatin will be analysis, Default is all

chrstart

where will start the analysis in the chromatin, default = 0

chrend

where will end the analysis in the chromatin, when set 0, the whole chromatin will be analysed. default = 0

resolution

the resolution of Hi-C dataset.

bedWindow

the window of sites, Default is 0

netplot

draw the network plot,when node number is too much,it may be not working. default = TRUE

net_layout

the layout of net plot, can be choose from layout.auto,layout.circle and layout.fruchterman.reingold. default = layout.fruchterman.reingold

NetClusterType

the method of topological clustering, can be choose from NULL,multileve,edgeBetweenness,walktrap,labelPropagation. default = multileve

NetVertexSize

network vertex size. default = 2

NetVertexChangeSize

the parameter to change the node vertex, can be choose from NULL,degree,closeness,betweenness,Local_cluster_coefficient,Eigenvector_centrality. default = degree

NetVertexLableDist

distance between label and vertex in the network. default = 0.1

NetVertexColor

the color of vertex. default = #7fbc41

NetVertexLabelCex

the size of network vertex label. default = 0.3

if_threshold

the threshold of interacion readcounts, default = 0

Details

HBP maps sequence sites of interest to the probability matrix, and calculate the interaction frequency and pinpoint the interaction networks mediated by these sites. The igraph package was used to plot an interaction network graph and make topological cluster analysis. According to the clustering results, users can classify all sites of interest into different types or clusters, and examine their potential differential properties respectively.

can be used as following command: network_analysis(bedFile="CTCF_hg19_encodeCluster_GM12878.bed",matrix_dir="CTCF_GM12878",chrom="chr1",chrstart=145000000,chrend=150000000,resolution=50)

network_analysis(bedFile="CTCF_hg19_encodeCluster_GM12878.bed",matrix_dir="CTCF_GM12878",outputpdf=TRUE,chrom="chr1",chrstart=145000000,chrend=150000000,resolution=50,bedWindow=0,net_layout="layout.auto",netplot=TRUE,NetClusterType="multileve",NetVertexSize=1,NetVertexChangeSize="degree",NetVertexLableDist=0.1,NetVertexColor="#7fbc41",NetVertexLabelCex=0.3,if_threshold=5)


HBP documentation built on July 7, 2017, 9:02 a.m.

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