Question: Positions to genes in minfi
0
gravatar for Asma rabe
2.9 years ago by
Asma rabe290
Japan
Asma rabe290 wrote:

Hi,

I used minfi package to analyze 450K methylation data. I got a list of regions that are differentially methylated.

I would like to know how can i convert the DMR regions into genes to asses which genes are hypo/hyper methylated.

Thank you.

genomicranges minfi • 422 views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Asma rabe290
Answer: Positions to genes in minfi
1
gravatar for James W. MacDonald
2.9 years ago by
United States
James W. MacDonald50k wrote:

Does ?nearest help you?

ADD COMMENTlink written 2.9 years ago by James W. MacDonald50k

Hi James,

nearest helped me to find the nearest gene to the DMR.

nearest(x, subject, select ="all")

returns all overlapping regions which are mostly redundant transcript, since i am interested in unique gene names I used

nearest(x, subject) #arbitrary is the default.

How to ensure that a single DMR (identified by bump hunter in minfi library ) is overlapping only with one gene? Is it possible that DMR overlaps with more than one gene?

Thank you.

ADD REPLYlink written 2.9 years ago by Asma rabe290
Answer: Positions to genes in minfi
0
gravatar for Asma rabe
2.9 years ago by
Asma rabe290
Japan
Asma rabe290 wrote:

Hi James,

nearest helped me to find the nearest gene to the DMR.

nearest(x, subject, select ="all")

returns all overlapping regions which are mostly redundant transcript, since i am interested in unique gene names I used

nearest(x, subject) #arbitrary is the default.

How to ensure that a single DMR (identified by bump hunter in minfi library ) is overlapping only with one gene? Is it possible that DMR overlaps with more than one gene?

Thank you.

 

ADD COMMENTlink written 2.9 years ago by Asma rabe290
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