Tutorial: Epigenomics RoadMap Project files now accessible via AnnotationHub
7
3.7 years ago by
Sonali Arora370
United States
Sonali Arora370 wrote:

Files from Epigenomics RoadMap Project have been added to AnnotationHub.

This vignette inside AnnotationHub gives you a quick tour on how to access these files  via the Hub with some examples.

Please let us know if you'd like any other files to be added to the Hub from the same project or another.

Thanks and Regards,

Sonali

modified 21 months ago by vanesa_12300 • written 3.7 years ago by Sonali Arora370

Hi Sonali, are there any plans to add access to the raw data (ie consolidated and unconsolidated tagAlign files) through AnnotationHub? As far as I can tell, this info is not indexed in a publicly accessible way and the easiest method currently is just to parse the file names from the web server HTML. Also, does AnnotationHub provide any methods to download files to disk rather than straight into R? Obviously for large BAM-type files working in memory is not always an option.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Malcolm Perry40
1

cache(hub["AH12345"]) retrieves the resource(s) to local disk (if necessary) and returns the path. Mostly large files are not read in to R, but returned in a format that can be queried for relevant information (as with the fasta file vignette example).

ADD REPLYlink written 3.1 years ago by Martin Morgan ♦♦ 22k

Dear Sonali,

I just posted a question regarding some Roadmap files: AnnotationHub: confusing pValue/qValue for (some) Roadmap records

Many thanks in advance,
Kevin

I've responded to this question at AnnotationHub: confusing pValue/qValue for (some) Roadmap records

Valerie