Create Network Object.

Usage

CreateNetworkObject(LinkageObject, genelist_idtype, filter_col, filter_value)

Arguments

LinkageObject: An Linkage Object after MultipleMotifAnalysis.
genelist_idtype: There are ensembl_gene_id, external_gene_name, entrezgene_id types of genetic IDs to choose from.
filter_col: p_value,FDR,rho can be selected.
filter_value: Cutoff value of filter_col.

Value

Network Object.

Examples

library(linkage)
library(LinkageData)
ATAC.seq <- BreastCancerATAC()
RNA.seq <- BreastCancerRNA()
LinkageObject <-
  CreateLinkageObject(
    ATAC_count = ATAC.seq,
    RNA_count = RNA.seq,
    Species = "Homo",
    id_type = "ensembl_gene_id"
  )
gene_list <- c("TSPAN6", "CD99", "KLHL13")
LinkageObject <-
  RegulatoryPeak(
    LinkageObject = LinkageObject,
    gene_list = gene_list,
    genelist_idtype = "external_gene_name"
  )
LinkageObject <-
  MultipleMotifAnalysis(LinkageObject = LinkageObject,
                        Species = "Homo",
                        TF_cor_method = "pearson")
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
#> Warning: the standard deviation is zero
LinkageObject <-
  CreateNetworkObject(
    LinkageObject = LinkageObject,
    genelist_idtype = "entrezgene_id",
    filter_col = "FDR",
    filter_value = 0.01
  )