conformation_network: Build Network from Conformation Peaks.

In pageRank: Temporal and Multiplex PageRank for Gene Regulatory Network Analysis

Description

Build network from conformation, e.g. HiChIP records.

Usage

conformation_network(
  table,
  promoter,
  pfm,
  genome,
  range = 500,
  p.cutoff = 5e-05,
  w = 7
)

Arguments

table	(data.frame) Records, with "Chr1", "Position1", "Strand1", "Chr2", "Position2" and "Strand2" in column name, and record 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.
range	(numeric) Search radius from "Position1" and "Position2" for promoters.
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 ([e-mail])

Examples

table <- data.frame(Chr1=c("chr1", "chr1"),
                    Position1=c(569265, 713603),
                    Strand1=c("+", "+"),
                    Chr2=c("chr4", "chr1"),
                    Position2=c(206628, 715110),
                    Strand2=c("+", "-"),
                    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)
conformation_network(table, promoter, pfm, "BSgenome.Hsapiens.UCSC.hg19")

pageRank documentation built on Nov. 8, 2020, 6:52 p.m.