An R package for listening genomic annotations.
- R plus GenomicRanges package
- Midicomp
- Timidity
Basic steps to reveal genomic symphony.
- Build a database with
GenomicRangespackage - Define
TrackandSymphonyobjects - Compile and listen your
midfile
- Clone this repo to setup your working directory.
git clone https://github.com/fgajardoe/genomidi.git
cd genomidi
- Setup your
datafolder
cd data
wget ... # all annotations you wish
- Get the docker image
docker pull fgajardoe/genomidi:latest
Alternatively you can build it your own with the Dockerfile included in the repository.
- Write your genomic symphony.
An example file is included in symphony.R.
Make sure your files in data/ are the same declared in your script.
- Compile and get your
midfile
docker run -it -v `pwd`:/home/genomidi/ fgajardoe/genomidi:lastest Rscript symphony.R
Where pwd is your working directory (that is, the root of this repository).
A Track object represents a set of genomic annotations of the same type, for example, the information you get from a bed file for genes, or transposable elements, or CHIPseq peaks, and so on.
Track.genes=Track(
DB=db.gr,
Aes=list(Name="names", Note="note", Vol="fixed_vol"),
Name="Gene",
Channel=1,
Instrument=1 # Piano
)
There is a few things to have in mind while setting up a Track object:
In construction
S=Symphony(
Label="The-repetitive-order",
Chr="chr19",
Start=19490627,
End=20123884,
Tempo=100000,
TrackList=list(T.ATAC,T.GENE,T.LINE,T.SINE,T.DNA,T.LTR)
)
GPLv3