Finding the regulatory peak of genes.

Usage

RegulatoryPeak(
  LinkageObject,
  gene_list,
  genelist_idtype,
  range = 5e+05,
  cor_method = "spearman",
  filter_col = "FDR",
  filter_value = 0.05
)

Arguments

LinkageObject: An Linkage Object.
gene_list: Character value,The gene you want to query.
genelist_idtype: There are ensembl_gene_id, external_gene_name, entrezgene_id types of genetic IDs to choose from.
range: Expand the range of genes to find regulatory peaks.
cor_method: For correlation calculation, pearson/spearman/kendall can be selected.
filter_col: p_value,FDR,rho can be selected.
filter_value: Cutoff value of filter_col.

Value

Regulate the peak list

Examples

library(linkage)
data("SmallLinkageObject")
gene_list <- c("TSPAN6", "CD99", "KLHL13")
LinkageObject <-
  RegulatoryPeak(
    LinkageObject = SmallLinkageObject,
    gene_list = gene_list,
    genelist_idtype = "external_gene_name"
  )