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jokergoo / rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions
https://jokergoo.github.io/rGREAT
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GREAT has more statistical columns that aren't visible #2

Closed semenko closed 8 years ago

semenko commented 8 years ago

I'm trying to sort & filter data based on some other columns that GREAT provides (e.g. BinomFdrQ & HyperBonfP / HyperFdrQ).

I don't see these in the current output of rGREAT -- perhaps they could be added? (They might be new in 3.0)

It looks like the output is: Ontology ID Desc BinomRank BinomP BinomBonfP BinomFdrQ RegionFoldEnrich ExpRegions ObsRegions GenomeFrac SetCov HyperRank HyperP HyperBonfP HyperFdrQ GeneFoldEnrich ExpGenes ObsGenes TotalGenes GeneSetCov TermCov Regions Genes

jokergoo commented 8 years ago

For these columns, although they are provided in the HTML table, but they are not available in the JSON file which rGREAT uses (only raw p-values are provided in the JSON file). However, it is easy to calculate these adjusted p-values in R. e.g. to get the FDR, use p.adjust(tb$BinomP, method = "BH"), to get the Bonferroni corrected p-value, use p.adjust(tb$BinomP, method = "bonferroni").

semenko commented 8 years ago

Awesome -- many thanks! (I saw them from the raw curl "interface" at http://bejerano.stanford.edu/help/display/GREAT/Programming+Interface )