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nsheff / LOLA

Locus Overlap Analysis: Enrichment of Genomic Ranges
http://code.databio.org/LOLA
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gettingStarted.Rmd #4

Closed fhalbritter closed 9 years ago

fhalbritter commented 9 years ago

gettingStarted.Rmd

regionDB = loadRegionDB(dbPath) Found collections: ucsc_example In 'ucsc_example', found index file:/home/fhalbritter/R/x86_64-unknown-linux-gnu-library/3.1/LOLA/extdata/hg19/ucsc_example/index.txt Found collections: ucsc_example In 'ucsc_example', no collection file. ucsc_example ::Loading cache:: /home/fhalbritter/R/x86_64-unknown-linux-gnu-library/3.1/LOLA/extdata/hg19/ucsc_example/ucsc_example.RData

nsheff commented 9 years ago

Yes, this is right. Please explain the issue... ?

-Nathan

On 04/20/2015 03:11 PM, Florian Halbritter wrote:

gettingStarted.Rmd

regionDB = loadRegionDB(dbPath)
Found collections: ucsc_example
In 'ucsc_example', found index
file:/home/fhalbritter/R/x86_64-unknown-linux-gnu-library/3.1/LOLA/extdata/hg19/ucsc_example/index.txt
Found collections: ucsc_example
In 'ucsc_example', no collection file.
ucsc_example
::Loading cache::
/home/fhalbritter/R/x86_64-unknown-linux-gnu-library/3.1/LOLA/extdata/hg19/ucsc_example/ucsc_example.RData

— Reply to this email directly or view it on GitHub https://github.com/sheffien/LOLA/issues/4.

fhalbritter commented 9 years ago

Oh, I see, this is the intended behaviour?

I guess I was confused by the output. "Found collections: ucsc_example" appears to contradict "In 'ucsc_example', no collection file.". Perhaps some paraphrasing would help?

What added to my confusion was that only one out of the five example region sets has a description in regionDB$description. That led me to believe that the data was incompletely loaded in the first stage. I would expect an example dataset to be reasonably complete in terms of annotations. At the moment, I have to guess what the different datasets are.