BuildNetwork.
BuildNetwork.Rd
BuildNetwork.
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")
#>
#> Attaching package: 'Biostrings'
#> The following object is masked from 'package:base':
#>
#> strsplit
#>
#> Attaching package: 'rtracklayer'
#> The following object is masked from 'package:BiocIO':
#>
#> FileForFormat
#> 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
)
BuildNetwork(LinkageObject)