Create a Linkage Object

Create a Linkage Object

Usage

CreateLinkageObject(ATAC_count, RNA_count, Species, id_type)

Arguments

ATAC_count

The chromatin accessibility matrix file is a tab-delimited multi-column data matrix as well, which the first three columns represent chromosome name, start coordinate on the chromosome and end coordinate on the chromosome of the peaks respectively; the remaining columns of the chromatin accessibility matrix file represent normalized or raw chromatin accessibility levels of peaks for each sample.

RNA_count

The gene expression matrix file is a tab-delimited multi-column data matrix, which the first column represents gene symbols and the following columns represent normalized or raw expression levels of genes for each sample.

Species

Select the species, Homo or Mus.

id_type

The RNA_count gene id type. There are ensembl_gene_id, external_gene_name, entrezgene_id types of genetic IDs to choose from.

Value

A Linkage 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"
  )