Description Usage Arguments Value Author(s) Examples
View source: R/conformation_network.R
Build network from conformation, e.g. HiChIP records.
1 2 3 4 5 6 7 8 9 | 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)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | 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")
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