TFBS_FANTOM: Creates a TFBS motif track from FANTOM

In TiphaineCMartin/coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

Creates a TFBS motif track from FANTOM

Description

Creates a track of TFBS motifs from FANTOM using the Gviz bioconductor package. A complete list of features and their associated colours can be found in the user guide.

Usage

TFBS_FANTOM(gen, chr, start, end, bedFilePath,title="TF motif FANTOM5")

Arguments

gen	the name of the genome.
chr	The chromosome of interest
start	The starting position in the region of interest (the smallest value)
end	The end position in the region of interest (the largest value)
bedFilePath	The path of the BED file from Kheradpour and Kellis, 2014.
title	The name of the annotation track

Value

An AnnotationTrack object of Gviz

Author(s)

Tiphaine Martin

References

http://bioconductor.org/packages/release/bioc/html/Gviz.html

Got to BindingMotifsBiomart binding motif biomart

Examples

library("Gviz")
gen <- "hg19"
chr<- "chr1"
start <- 6000000
end <- 6500000

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
AP1FantomFile <- file.path(extdata, "FANTOM/Fantom_hg19.AP1_MA0099.2.sites_example970.txt")

if(interactive()){
  tfbsFANTOMtrack <- TFBS_FANTOM(gen,chr,start, end, AP1FantomFile)
  plotTracks(tfbsFANTOMtrack, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
} else {
  data(tfbsFANTOMtrack)
  plotTracks(tfbsFANTOMtrack, from = start, to = end,
                                   fontfamily="sans",fontfamily.title="sans")
}

TiphaineCMartin/coMET documentation built on April 27, 2022, 6:45 a.m.