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jokergoo / rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions
https://jokergoo.github.io/rGREAT
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Explanation of result columns #35

Closed dktanwar closed 1 year ago

dktanwar commented 1 year ago

Hi @jokergoo

Thanks for rGREAT, extremely useful.

I was looking into difference between p_value and p_value_hyper, but I was not able to find it in the vignette. Could you please help me with this?

id description genome_fraction observed_region_hits fold_enrichment p_value p_adjust mean_tss_dist observed_gene_hits gene_set_size fold_enrichment_hyper p_value_hyper p_adjust_hyper
GO:0042254 ribosome biogenesis 0.01304709 4 7.861071097 0.001655518 0.346003327 4116 3 6 2.756410256 0.075978557 1
GO:0022613 ribonucleoprotein complex biogenesis 0.01615005 4 6.350698889 0.003565088 0.372551657 4116 3 7 2.362637363 0.115906015 1
GO:0022607 cellular component assembly 0.01097845 3 7.006733622 0.009006156 0.470571658 3775 2 7 1.575091575 0.37186203 1
GO:0065003 protein-containing complex assembly 0.01097845 3 7.006733622 0.009006156 0.470571658 3775 2 5 2.205128205 0.224480679 1
GO:0043933 protein-containing complex organization 0.015571808 3 4.939893788 0.022744111 0.950703858 3775 2 6 1.837606838 0.29873174 1
GO:0006364 rRNA processing 0.008926099 2 5.74518061 0.047484017 1 4916 2 5 2.205128205 0.224480679 1
dktanwar commented 1 year ago

Found them here: https://great-help.atlassian.net/wiki/spaces/GREAT/pages/655456/Statistics

liboxun commented 10 months ago

Echoing @dktanwar, thanks for rGREAT @jokergoo!

I had the same exact question, and I'm so glad to find the answer here. However, it'd still be very useful if descriptions of what each result column means are included in the documentation of rGREAT.