User: haiying.kong
haiying.kong • 290
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Posts by haiying.kong
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... library(KEGGREST)
> names(keggGet("map07049")[[1]])
[1] "ENTRY" "NAME" "PATHWAY_MAP" "COMPOUND" "REFERENCE"
I need to get gene list (hugo-symbol) in each pathway. How can I get this from KEGGREST?
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platf ...
written 23 months ago by
haiying.kong • 290
• updated
23 months ago by
Damian Kao ♦ 15k
0
votes
2
answers
596
views
2
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... Thank you very much for your reply.
I have whole exome sequence data from matched blood and tumor samples, used Mirkat to identify somatic structural variations, then annotated them with gene names. ...
written 23 months ago by
haiying.kong • 290
3
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2
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596
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6 follow
2
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... I found structural variations from WES data. The top frequency genes are almost all pseudogenes.
Could anyone please give me any advice? ...
written 23 months ago by
haiying.kong • 290
• updated
23 months ago by
d-cameron • 2.1k
1
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0
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558
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0
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Comment:
C: R survivalsvm package
... Not really. It is a general question about the software tool.
For instance, if I run the example code on the manual of the software, the predicted values are:
> pred.survsvm.reg$predicted
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 13.88731 14.94699 11.12112 ...
written 23 months ago by
haiying.kong • 290
2
votes
0
answers
558
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0
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... Dear All,
I am trying to use the R package: survivalsvm.
I can get it running without error, survivalsvm and predict.survival, but if I look at the predicted values from the output of predict.survivalsvm, the values are not easy to interpret. They did not look like expected relapse time, or pro ...
written 23 months ago by
haiying.kong • 290
0
votes
2
answers
141
views
2
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... Then, he will say:
You are making excuse to be lazy! ...
written 2.1 years ago by
haiying.kong • 290
0
votes
2
answers
141
views
2
answers
... Thanks for the advice.
If I run, there will be no driver genes identified. So nothing can be included in any paper that can be published. Just waste of my time.
But I will keep the email anyway. ...
written 2.1 years ago by
haiying.kong • 290
0
votes
2
answers
141
views
2
answers
... Such communication is impossible with such dense head, sorry to say this word.
After "because", there will be scientific explanation that involves statistics, and he refuses to hear any bioinformatics, or statistics, or mathematics in any occasion. He is 100000% pure biologist. ...
written 2.1 years ago by
haiying.kong • 290
1
vote
1
answer
433
views
1
answer
... It was very hot several years back. Is it still hot field?
I feel much is done in this field, and nothing original is coming out. ...
written 2.1 years ago by
haiying.kong • 290
• updated
2.1 years ago by
Devon Ryan ♦ 94k
0
votes
1
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1.6k
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1
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... Thanks again for your help.
It takes very very long to run MuTect even with many cores or nodes. So I do not have time to rerun, because I am trying to finish up soon.
Is there any way to do the filtering from MuTect output? ...
written 2.2 years ago by
haiying.kong • 290
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