epiNetwork: Construct co-epihet network based on DEH loci.
In epihet: Determining Epigenetic Heterogeneity from Bisulfite Sequencing Data

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.

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)

`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)

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.

epihet documentation built on Dec. 31, 2020, 2:01 a.m.