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Question: CHiPpeakAnno GO and/or KEGG results presenting
0
gravatar for lokapal
19 months ago by
lokapal0
lokapal0 wrote:

  Hello, developers and Bioconductor experts! :-)

I'm trying to annotate my genomic features track (bed format) and build for annotated data gene ontology and/or KEGG pathway. Right now I'm using CHiPpeakAnno package. All is working as it should be (as it seems to me). My problem is that I cannot use the results and manual, unfortunately, doesn't cover it. I loaded my dataset to GRanges, annotated it (by the way, what database is the better for H. sapiens annotations?) and built GO with function getEnrichedGO. How can I use the full results? I mean how to build from "over" object/result something like to this figure:

KEGG results graph

Thanks in advance!

 
ADD COMMENTlink modified 19 months ago • written 19 months ago by lokapal0
0
gravatar for Julie Zhu
19 months ago by
Julie Zhu3.8k
United States
Julie Zhu3.8k wrote:
Lokapal, Thanks for the feedback! Jianhong is working on adding plot functions and documentation. He will get back to you soon. Best regards, Julie From: "lokapal [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> Reply-To: "reply+d56803e8+code@bioconductor.org<mailto:reply+d56803e8+code@bioconductor.org>" <reply+d56803e8+code@bioconductor.org<mailto:reply+d56803e8+code@bioconductor.org>> Date: Friday, April 15, 2016 5:20 AM To: Lihua Julie Zhu <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>> Subject: [bioc] CHiPpeakAnno GO and/or KEGG results presenting Activity on a post you are following on support.bioconductor.org<https: urldefense.proofpoint.com="" v2="" url?u="&lt;a href=" http:="" <a="" href="http://https-3A__support.bioconductor.org" rel="nofollow">https-3A__support.bioconductor.org"="" rel="nofollow">https-3A__support.bioconductor.org&d=BQMDaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=-9KMl56P5J-j5fKZSa2kO8v6uFDPMqhSlQqerK6cfyo&s=H0j2ZmrVhhUbXCdwdh3V2P62Hz7PKaILwXAC-mJFiSo&e="> User lokapal<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_u_10101_&amp;d=BQMDaQ&amp;c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&amp;r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&amp;m=-9KMl56P5J-j5fKZSa2kO8v6uFDPMqhSlQqerK6cfyo&amp;s=PEtEWHIq5dIPJGsVrdW7tAXy9dA3ZRKYHwe0zA9c1qs&amp;e="> wrote Question: CHiPpeakAnno GO and/or KEGG results presenting<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_80861_&amp;d=BQMDaQ&amp;c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&amp;r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&amp;m=-9KMl56P5J-j5fKZSa2kO8v6uFDPMqhSlQqerK6cfyo&amp;s=0gdYgO1LbAMs5RgQEg31XyEhsklxjpHzLmDXAEtoEjc&amp;e=">: Hello, developers and Bioconductor experts! :-) I'm trying to annotate my genomic features track (bed format) and build for annotated data gene ontology and/or KEGG pathway. Right now I'm using CHiPpeakAnno package. All is working as it should be (as it seems to me). My problem is that I cannot use the results and manual, unfortunately, doesn't cover it. I loaded my dataset to GRanges, annotated it (by the way, what database is the better for H. sapiens annotations?) and built GO with function getEnrichedGO. How can use the full results? I mean how to build from "over" object/result something like to this figure: [KEGG results graph] Thanks in advance! ________________________________ Post tags: chippeakanno, go, kegg, graphics You may reply via email or visit CHiPpeakAnno GO and/or KEGG results presenting
ADD COMMENTlink written 19 months ago by Julie Zhu3.8k

Hello, Julie!

Thanks a lot for prompt answer. If I сould can give you advice concerning CHiPpeakAnno documentation - it would be wise to create section "Working Recipes" and, probably, reorganize "User guide" according to its appearance. It's especially important for annotation and further getEnrichedGO and/or getEnrichedPATH processing because this functions contain some non-obvious parameters (e.g. multiAdjMethod description is as follows: "The multiple testing procedures, for details, see mt.rawp2adjp in multtest package". From mt.rawp2adjp description we can see that "This function computes adjusted p-values for simple multiple testing procedures from a vector of raw (unadjusted) p-values". Right now it is unclear should we use this method or not and in what cases (I can only guess that this option should be used in the case of mix in one GRange object different genomic tracks). I only know that old CHiPpeakAnno description (e.g. from Bioconductor 2.11) contains the other usage example:

enrichedGO = getEnrichedGO (annotatedPeak, orgAnn="org:Hs:eg:db", maxP=0.01, multiAdj=TRUE, minGOterm=10, multiAdjMethod="BH")

So multiAdj option changed its default behaviour. Why? What should we use?

As for total usage it is not obvious from the manual that there are two (or even three if biomart is included) quite different workflows. As a matter of fact single mention in the user guide about it is the following statement: "If you are using TxDb as annotation data, please try to change feature_id_type to “entrez_id”. Moreover it would be good to have some very brief and concise comparison of different databases (as for your module, of course). It would be good to have in the "Recipes" section completely working examples for each workflow.

      I do understand that all my questions and problems looks like quite trivial to you, but I assure you that not all CHiPpeakAnno users are hard gene annotators and pathway investigators/creators. We are not so cool in this area of science so we would like to have a bit of help in the manual.

    Anyway thanks for very useful package!

ADD REPLYlink modified 19 months ago • written 19 months ago by lokapal0
Lokapal, Many thanks for your constructive feedback! We will incorporate your suggestions to our documentation. FYI, Jianhong and Jun have been working on adding more examples to the documentation. Please take a look at http://bioconductor.org/packages/devel/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.html and http://bioconductor.org/packages/devel/bioc/vignettes/ChIPpeakAnno/inst/doc/quickStart.html Regarding function parameters, I am also against parameter changes unless there is an overwhelming benefit of changing. Regarding getEnrichedGO, I suggest use multiAdj=TRUE, multiAdjMethod="BH" and fine tune maxP . Thanks again for helping us make ChIPpeakAnno more user friendly! Best regards, Julie From: "lokapal [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> Reply-To: "reply+dbc406ed+code@bioconductor.org<mailto:reply+dbc406ed+code@bioconductor.org>" <reply+dbc406ed+code@bioconductor.org<mailto:reply+dbc406ed+code@bioconductor.org>> Date: Friday, April 15, 2016 1:35 PM To: Lihua Julie Zhu <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>> Subject: [bioc] C: CHiPpeakAnno GO and/or KEGG results presenting Activity on a post you are following on support.bioconductor.org<https: urldefense.proofpoint.com="" v2="" url?u="&lt;a href=" http:="" <a="" href="http://https-3A__support.bioconductor.org" rel="nofollow">https-3A__support.bioconductor.org"="" rel="nofollow">https-3A__support.bioconductor.org&d=BQMDaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=LW3YGiFXfLVIWX_aTr-o7bPuhreiIYsPdJRGN5aS1UQ&s=zaE9GIp-ARpILJ70N4I1sJuipalTbnaah0UN_k9JKRQ&e="> User lokapal<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_u_10101_&amp;d=BQMDaQ&amp;c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&amp;r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&amp;m=LW3YGiFXfLVIWX_aTr-o7bPuhreiIYsPdJRGN5aS1UQ&amp;s=oT8nd3LrH4OurjVp122rD6bu5X5rSE8QImgseUuGR60&amp;e="> wrote Comment: CHiPpeakAnno GO and/or KEGG results presenting<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_80861_-2380898&amp;d=BQMDaQ&amp;c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&amp;r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&amp;m=LW3YGiFXfLVIWX_aTr-o7bPuhreiIYsPdJRGN5aS1UQ&amp;s=naogxwiE9chQxF5yoM7e4SbSdwLMfNvDjZPaF7Vqyt0&amp;e=">: Hello, Julie! Thanks a lot for prompt answer. If I would can give you advice concerning CHiPpeakAnno documentation - it would be wise to create section "Working Recipes" and, probably, reorganize "User guide" according to its appearance. It's especially important for annotation and further getEnrichedGO and/or getEnrichedPATH processing because this functions contains some non-obvious parameters (e.g. multiAdjMethod description is as follows: "The multiple testing procedures, for details, see mt.rawp2adjp in multtest package". From mt.rawp2adjp description we can see that "This function computes adjusted p-values for simple multiple testing procedures from a vector of raw (unadjusted) p-values". Right now it is unclear should we use this method or not and in what cases (I can only guess that this option should be used in the case of mix in one GRange object different genomic tracks). I only know that old CHiPpeakAnno descriptions (e.g. from Bioconductor 2.11) contains the other usage example: enrichedGO = getEnrichedGO (annotatedPeak, orgAnn="org:Hs:eg:db", maxP=0.01, multiAdj=TRUE, minGOterm=10, multiAdjMethod="BH") So multiAdj option changed its default behaviour. Why? What we should use? As for total usage it is not obvious from the manual that there are two (or even three if biomart is included) quite different workflows. As a matter of fact single mention in the user guide about it is the following statement: "If you are using TxDb as annotation data, please try to change feature_id_type to �entrez_id�. Moreover it would be good to have some very brief and concise comparison of different databases (as for your module, of course). It would be good to have in the "Recipes" section completely working examples for each workflow. I do understand that all my questions and problems looks like quite trivial to you, but I assure you that not all CHiPpeakAnno users are hard gene annotators and pathway investigators/creators. We are not so cool in this area of science so we would like to have a bit of help in the manual. Anyway thanks for very useful package! ________________________________ Post tags: chippeakanno, go, kegg, graphics You may reply via email or visit C: CHiPpeakAnno GO and/or KEGG results presenting
ADD REPLYlink written 19 months ago by Julie Zhu3.8k
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