accessibility_network {pageRank}R Documentation

Build Network from Accessibility Peaks.

Description

Build network from accessibility, e.g. ATAC-Seq peaks.

Usage

accessibility_network(table, promoter, pfm, genome, p.cutoff = 5e-05, w = 7)

Arguments

table

(data.frame) Peaks, with "Chr", "Start" and "End" in column name, and peak ID in row names.

promoter

(GRanges) Promoter regions.

pfm

(PFMatrixList) Positon Frequency Matrices (PFMs) of regulators.

genome

(BSgenome or character) Genome build in which regulator motifs will be searched.

p.cutoff

(numeric) P-value cutoff for motifs searching within peaks for TF identificaton.

w

(numeric) Window size for motifs searching within peaks for TF identificaton.

Value

(data.frame) Network, with "reg" and "target" in column name.

Author(s)

DING, HONGXU (hd2326@columbia.edu)

Examples


table <- data.frame(Chr=c("chr1", "chr1"), Start=c(713689, 856337),
                    End=c(714685, 862152), row.names=c("A", "B"),
                    stringsAsFactors=FALSE)
regulators=c("FOXF2", "MZF1")
#peaks and regulators to be analyzed

library(GenomicRanges)
library(GenomicFeatures)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(org.Hs.eg.db)
library(annotate)
promoter <- promoters(genes(TxDb.Hsapiens.UCSC.hg19.knownGene))
names(promoter) <- getSYMBOL(names(promoter), data="org.Hs.eg")
promoter <- promoter[!is.na(names(promoter))]
#get promoter regions

library(JASPAR2018)
library(TFBSTools)
library(motifmatchr)
pfm <- getMatrixSet(JASPAR2018, list(species="Homo sapiens"))
pfm <- pfm[unlist(lapply(pfm, function(x) name(x))) %in% regulators]
#get regulator position frequency matrix (PFM) list

library(BSgenome.Hsapiens.UCSC.hg19)
accessibility_network(table, promoter, pfm, "BSgenome.Hsapiens.UCSC.hg19")
#generate network


[Package pageRank version 1.2.0 Index]