PeakToGene: Get peak to gene links

In CostaLab/scMEGA: Single-cell Multiomic Enhancer-based Gene Regulatory Network Inference

Get peak to gene links

Description

This function will link peak to genes based on correlation analysis. We here modified the code from the ArchR package of the addPeak2GeneLinks function to make it compatible with matrix input. For more details, please refer to https://www.archrproject.com/reference/addPeak2GeneLinks.html.
Author: Jeffrey Granja

Usage

PeakToGene(
  peak.mat,
  gene.mat,
  genome = "hg19",
  max.dist = 250000,
  method = "corrleation"
)

Arguments

peak.mat	A matrix containing chromatin accessibility data
gene.mat	A matrix containing gene expression data
genome	Which genome to use. Currently available are: hg19, hg38, mm9, and mm10
max.dist	The maximum distance between a peak and a gene. Default: 250000 bp
method	Which method to use to measure the association between peak and gene. Available are: "correlation", "glm"

Value

A data frame containing all peak-to-gene links

CostaLab/scMEGA documentation built on Sept. 25, 2024, 6:11 a.m.