coMET (version 1.4.4)

TFBS_FANTOM: 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)

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.

Value

An AnnotationTrack object of Gviz

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.txt")

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