conformation_network {pageRank} | R Documentation |
Build network from conformation, e.g. HiChIP records.
conformation_network( table, promoter, pfm, genome, range = 500, p.cutoff = 5e-05, w = 7 )
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. |
(data.frame) Network, with "reg" and "target" in column name.
DING, HONGXU (hd2326@columbia.edu)
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")