epiNetwork: Construct co-epihet network based on DEH loci.

In TheJacksonLaboratory/epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

Description

Construct co-epihet network for DEH loci or for genes with genome region containing DEH loci using WGCNA and identify modules that are significantly associated with the measured clinical traits for co-epihet DEH loci network,we identify genes with genome region containing DEH loci in each module.

Usage

epiNetwork(node.type = "locus", DEH, compare.matrix, value = "pdr",
  group, subtype, datTraits = NULL, annotation.obj,
  networktype = "signed", method = "pearson", prefix = NULL,
  mergeCutHeight = 0.25, minModuleSize = 30)

Arguments

node.type	a character suggest node type in network. Possible values are 'locus','gene' (default:locus)
DEH	the dataframe containing the chromosome number, loci and strand information of DEH loci generated from diffHet() function
compare.matrix	The comparison matrix generated from the compMatrix() function.
value	A character, which is used to identify DEH loci. Possible values are 'pdr', 'epipoly',and 'shannon'(default:pdr)
group	The subtype group to be used to construct network
subtype	A dataframe containing the subtype information for the samples in the comparison matrix. The row names should be the names of the samples and there should be one column containing the subtype information for each sample
datTraits	a dataframe containing the clinical traits for all patients from the subtype group
annotation.obj	a GRanges object containing gene annotation information
networktype	network type in WGCNA (default:signed)
method	character string specifying the correlation to be used in WGCNA (default:pearson)
prefix	character string containing the file name base for files containing the consensus topological overlaps in WGCNA
mergeCutHeight	a numeric, dendrogram cut height for module merging (default: 0.25)
minModuleSize	a numeric, minimum module size for module detection in WGCNA (default: 30)

Value

a list, if node type is CpG site, it contains the epigenetic heterogeneity matrix for patients module information, gene.list which is a data frame containing genes with genome region containing DEH loci from one module if node type is gene,it contains the epigenetic heterogeneity matrix for patients and module information.

TheJacksonLaboratory/epihet documentation built on Dec. 22, 2020, 1:10 p.m.