MotifAnalysis.
MultipleMotifAnalysis.Rd
MotifAnalysis.
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.
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