TFBS_FANTOM: Creates a TFBS motif track from FANTOM

Description Usage Arguments Value Author(s) References Examples

View source: R/BiofeatureGraphics.R

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

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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

Author(s)

Tiphaine Martin

References

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

Got to BindingMotifsBiomart binding motif biomart

Examples

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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)
}

coMET documentation built on Nov. 23, 2017, 2:05 a.m.