User: saadmurtazakhan

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United States
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Posts by saadmurtazakhan

<prev • 26 results • page 1 of 3 • next >
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How to arrive at an optimal value for attribute level in groupGO or enrichGO in clusterprofiler
... Hi , I am trying to use your R package clusterprofiler. My question is with regards to groupGO function. I was wondering what would be a good value to use for "level" attribute in the function. Or is there a way to arrive at the most optimal value for the attribute "level". thanks  ggo <- gro ...
clusterprofiler groupgo gene ontology level written 8 weeks ago by saadmurtazakhan10 • updated 8 weeks ago by Guangchuang Yu990
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... So whats explains the reason for so many gene pairs having value 1? ...
written 18 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... Some of the genes where number of GO terms are not equal always return 1. Is that an accurate value for functional similarity to use? what can be possible turnaround for the same other than not considering those genes altogether? ...
written 18 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... Thanks that helps. ...
written 18 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... But in this example you still have to give semData as an argument. Should I give hsGO or mmGO as semData or would both yeild similar results? ...
written 18 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... I meant what should I specify as semData. In the vignette it uses hsGO as semdata. Since here the data is from two different species what should be semData here. ...
written 18 months ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... But mgoSim also takes semData as input. How do I bypass that? ...
written 18 months ago by saadmurtazakhan10
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Using GOsemsim to calculate semantic similarity between orthologus genes of two species
... Hi, I know this question has been asked before a long time ago and I don't see an answer of that question in the mailing list or in the vignette of GOsemsim package. So I was wondering what is the easiest possible way of calculating GO semantic similarity value for orthologus gene pairs between two ...
gosemsim gene ontology semantic similarity across species written 18 months ago by saadmurtazakhan10 • updated 18 months ago by Guangchuang Yu990
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Comment: C: Using mgeneSim with Ensembl ids
... What should I change below to make bitr work. bitr(mytestgenes, fromType="ENSEMBLID", toType="ENTREZID", OrgDb="org.Hs.eg.db") Error in bitr(mytestgenes, fromType = "ENSEMBLID", toType = "ENTREZID", : unused argument (OrgDb = "org.Hs.eg.db") ...
written 22 months ago by saadmurtazakhan10
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Comment: C: Using mgeneSim with Ensembl ids
... This is my session info. R version 3.3.0 (2016-05-03) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.7 (Final) locale: [1] C attached base packages: [1] stats     graphics  grDevices utils     datasets  methods   base      other attached packages: [1] GOSemSim_1.30.3     ...
written 22 months ago by saadmurtazakhan10

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