TFBS_FANTOM {coMET} | R Documentation

## 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)
    } else {
      data(tfbsFANTOMtrack)
      plotTracks(tfbsFANTOMtrack, from = start, to = end)
    }

[Package coMET version 1.12.0 Index]