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jokergoo / rGREAT

GREAT Analysis - Functional Enrichment on Genomic Regions
https://jokergoo.github.io/rGREAT
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use MSigDB database with rGREAT tool #18

Closed andreaT87 closed 5 years ago

andreaT87 commented 5 years ago

Dear rGREAT tool providers,

This is Andrea Terrasi (PhD student at LMU in Munich). I am working with your tool (last version) and for my data (mm10 genome) I don't have the possibility to use the MSigDB database as "available ontologies".

How is it possible? how can I select the MSigDB with your package Thank you for your support

andreaT87 commented 5 years ago

to better explain, I am going to attach the script:

head(sign_atac_sig1) chr start end 1 chr1 107488351 107488527 2 chr1 107748797 107748953 3 chr1 118449422 118449734 4 chr1 125496866 125497070 5 chr1 127261095 127261323 6 chr1 127357884 127358097

job_1 = submitGreatJob(sign_atac_sig1, bg = NULL,

  • species = "mm10",
  • includeCuratedRegDoms = TRUE,
  • rule = "basalPlusExt",
  • adv_upstream = 250.0,
  • adv_downstream = 250.0,
  • adv_span = 250.0,
  • request_interval = 10,
  • max_tries = 10,
  • version = "4.0.4") Warning message: In submitGreatJob(sign_atac_sig1, bg = NULL, species = "mm10", includeCuratedRegDoms = TRUE, : GREAT gives a warning: Your set hits a large fraction of the genes in the genome, which often does not work well with the GREAT Significant by Both view due to a saturation of the gene-based hypergeometric test.

See our tips for handling large datasets or try the Significant By Region-based Binomial view.

availableCategories(job_1) [1] "GO" "Phenotype" "Genes"

################### I hope that this could be usefoul. Thank you again for your suppoty

Best regards, Andrea Terrasi

jokergoo commented 5 years ago

I guess you need to use GREAT version 3.0.0. In 4.0.4, they remove quite a lot ontologies. See http://great.stanford.edu/help/display/GREAT/Version+History

You can use the old version of GREAT by sepcifying version = '3'.

andreaT87 commented 5 years ago

Dear Zuguang Gu, Thank you so much for your reply

Best, Andrea