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jokergoo / rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions
https://jokergoo.github.io/rGREAT
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The `getEnrichmentTables` only prints first 500 lines #29

Closed aseetharam closed 2 years ago

aseetharam commented 2 years ago

Hello,

Thanks for this package. It has been a lifesaver for running parameter optimization of one of the programs (yes, I go with a default interval of 60 seconds!).

So, when I downloaded the various enrichment tables (using getEnrichmentTables, I noticed that I'm only getting 500 lines exact (for the large queries for which I expect it to be much more than 500). I tried the option download_by = 'tsv' as well, but it did not make any difference. Am I doing something wrong?

Thanks,

jokergoo commented 2 years ago

The default use of getEnrichmentTables() should give you the complete table:

> tb = getEnrichmentTables(job)
> sapply(tb, nrow)
GO Molecular Function GO Biological Process GO Cellular Component
                 4219                 13145                  1726

If you specify download_by = 'tsv', there will be maximal 500 rows, which is restricted by GREAT server.

> tb = getEnrichmentTables(job, download_by = "tsv")
> sapply(tb, nrow)
GO Molecular Function GO Biological Process GO Cellular Component
                  500                   500                   500
aseetharam commented 2 years ago

Thank you for the clarification. I will leave out the download_by option from here on.

Thanks,