Description Usage Arguments Value Author(s) Examples
View source: R/accessibility_network.R
Build network from accessibility, e.g. ATAC-Seq peaks.
1 | accessibility_network(table, promoter, pfm, genome, p.cutoff = 5e-05, w = 7)
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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. |
(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 | 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
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