Description Usage Arguments Value Author(s) References Examples
View source: R/BiofeatureGraphics.R
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.
1 | TFBS_FANTOM(gen, chr, start, end, bedFilePath,title="TF motif FANTOM5")
|
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 |
An AnnotationTrack object of Gviz
Tiphaine Martin
http://bioconductor.org/packages/release/bioc/html/Gviz.html
Got to BindingMotifsBiomart binding motif biomart
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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)
}
|
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