Question: DeepBlueR - query all annotations across region
0
3 months ago by
Paul Shannon370
Paul Shannon370 wrote:

Just taking my first look at DeepBlueR, read the man pages and the vignette, ran through some of the examples. Good stuff here - but I am a little confused about formulating my typical queries.

For example, in naive pseudo-code, to obtain all the ChIP-seq hits in a small region of the hg38 genome:

tbl.hits <- query(deepblue, project="ChIP-atlas", genome="hg38",
region="chr2:233,054,878-233,112,822")


With this style of query - with no mention of experiment type, cell type, or antibody - I could obtain all the reported binding sites in the region, with any filtering (by cell type, score, or TF) as a subsequent step.

Could you point me in the right direction?

chip-seq queries • 86 views
modified 3 months ago by Bioconductor Community ♦♦ 0 • written 3 months ago by Paul Shannon370

Dear Paul,

Thanks for your interest in DeepBlueR. It's not entirely clear to me what you want to achieve. Could you please have a look at the usage example in the R package? They will probably give you an idea how these queries are constructed. Generally, you will have to combine a few commands to achieve your goal.

You can list available use cases via demo(package = "DeepBlueR")

You can trigger individual use case demonstrations for instance via demo(topic = "use_case1", package = "DeepBlueR")

You can also find the code for these usecases on github: https://github.com/MPIIComputationalEpigenetics/DeepBlueR/tree/master/demo

More examples and use cases can be found on the website: https://deepblue.mpi-inf.mpg.de/use_cases.php Note that these are not in R but should give you an idea how the commands have to be combined to achieve what you want.

Hope that helps! Let us know if you have any specific questions.