MotifAnalysis.

MotifAnalysis.

Usage

BuildGRNs(LinkageObject, Species = "Homo", TF_cor_method)

Arguments

LinkageObject

An Linkage Object after RegulatoryPeak.

Species

Select the species, Homo or Mus.The default is Homo.

TF_cor_method

For correlation calculation, pearson/spearman/kendall can be selected.

Value

An Linkage Object after BuildGRNs

Examples

library(Linkage)
LinkageObject <-
  CreateLinkageObject(
    ATAC_count = Small_ATAC,
    RNA_count = Small_RNA,
    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 <-
  BuildGRNs(LinkageObject = LinkageObject,
                        Species = "Homo",
                        TF_cor_method = "pearson")
#> 
#> Attaching package: 'Biostrings'
#> The following object is masked from 'package:base':
#> 
#>     strsplit
#> 
#> Attaching package: 'rtracklayer'
#> The following object is masked from 'package:BiocIO':
#> 
#>     FileForFormat