User: saadmurtazakhan

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United States
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Joined:
4 years, 11 months ago
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Posts by saadmurtazakhan

<prev • 30 results • page 1 of 3 • next >
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Comment: C: How to change the size of yaxis in motifstack
... @OU_jianhong is there a better work around than above. How Can I use ylim with plotmotifstack? ...
written 27 days ago by saadmurtazakhan10
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Comment: C: How to change the size of yaxis in motifstack
... That's probably not what I want. With ic.scale=TRUE ![With ic.scale=TRUE ][1] With ic.scale=FALSE ![With ic.scale=FALSE][2] [1]: https://live.staticflickr.com/65535/48578945027_b54cb84865_m.jpg [2]: https://live.staticflickr.com/65535/48578799501_34595bb968_m.jpg ...
written 27 days ago by saadmurtazakhan10
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Comment: C: How to change the size of yaxis in motifstack
... I have a motif and I am trying to look at the surrounding nucleotides distribution. So in the matrix I make all the motif positions to be zero and then look at the surrounding nucleotides but since they are too small I need to change the yaxis size. Please let me know how I go about in doing that. ...
written 29 days ago by saadmurtazakhan10
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How to change the size of yaxis in motifstack
... Hi, I am trying to use motifstack in bioconductor. I was wondering if there is any way to reduce the size of yaxis or limit the yaxis to a maximum value. I tried to use plotYaxis but I am unable to reduce the size of the yaxis. I was wondering how to do it. thanks Saad ...
motifstack plotmotiflogostack written 4 weeks ago by saadmurtazakhan10
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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 16 months ago by saadmurtazakhan10 • updated 16 months ago by Guangchuang Yu1.1k
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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 2.7 years 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 2.7 years ago by saadmurtazakhan10
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Comment: C: Using GOsemsim to calculate semantic similarity between orthologus genes of two
... Thanks that helps. ...
written 2.7 years 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 2.7 years 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 2.7 years ago by saadmurtazakhan10

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