Programmatic Overrepresentation Questions

[cross12tamu]

I am using Python to HTTP post and do multiple overrepresentation test. I have done so successfully. However, I have a few questions that are hopefully simple to answer.

1. Is there a way to gather some of the browser information that is calculated, such as the amount of IDs not mapped to PANTHER successfully, as well as Expected Values, and some others? Or are we limited to those inputs provided from the help page? Which, the listed inputs are "organism, geneList, enrichmentType, test_type, correction, type".

2. Is there a way to use a reference list, instead of the entire organism list? From what it seems, the post only takes the organism call, which the options are: "organism - Use PANTHER supported organism web service to determine list of sup[p]orted organisms. The long name is used as a parameter."

3. Is the organism list the same as the browser organism list?

Let me know if there are any questions, and I will answer them as soon as possible.

Thanks in advance,

Curtis

[huaiyumi]

Hi Chris, Can you assign this one to Anushya? I am not familiar with it. Huaiyu From: Chris Mungall <[email protected]> Reply-To: geneontology/panther-enrichment <[email protected]> Date: Thursday, March 14, 2019 at 3:27 PM To: geneontology/panther-enrichment <[email protected]> Cc: Huaiyu Mi <[email protected]>, Assign <[email protected]> Subject: Re: [geneontology/panther-enrichment] Programmatic Overrepresentation Questions (#9) Assigned #9<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_geneontology_panther-2Denrichment_issues_9&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=3nZTGjHGiC_7Cvdu7JnVDQ&m=AwC1_6kYMVBc2fahU7wKVfykaAendOMmHreyyuTlh_g&s=WzZ1tilk5gNR2UqdD8EcUqQmjX9RRO4cwNjiLSP7uIc&e=> to @huaiyumi<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_huaiyumi&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=3nZTGjHGiC_7Cvdu7JnVDQ&m=AwC1_6kYMVBc2fahU7wKVfykaAendOMmHreyyuTlh_g&s=sXowQVHZQJnqO6hta_DHG9Ma9ZMR9uPfVeH9UlpDjR0&e=>. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_geneontology_panther-2Denrichment_issues_9-23event-2D2205000649&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=3nZTGjHGiC_7Cvdu7JnVDQ&m=AwC1_6kYMVBc2fahU7wKVfykaAendOMmHreyyuTlh_g&s=caWELSkFi3MCmkugt5EYnHGOOhLczAwQX2YlcPiBqSU&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AGWGcBe1bhNYjg8vsHmkU2QsCZvo3SDcks5vWszQgaJpZM4XXrj4&d=DwMCaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=3nZTGjHGiC_7Cvdu7JnVDQ&m=AwC1_6kYMVBc2fahU7wKVfykaAendOMmHreyyuTlh_g&s=-weWmboYSg5oQN31zP52OImaYBzi_o493l69e-_pfbw&e=>.