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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?
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.