Question: RRBS analysis using methylkit with 2 variables
0
gravatar for maria2019
12 months ago by
maria2019100
maria2019100 wrote:

Hi,

I have 16 RRBS samples: 4 control-female, 4 control-male, 4 treatment female, 4 treatment-male.

I wanna analyse for DMR using methylkit.

I can easily divide them to two analysis (8 samples each) and perform one for female control vs treatment ,and male control vs treatment.

I however, want to also be able to normalize the methylation data among all samples and selected the bases that has been covered in all positions in all 16 samples, and then find the DMR for each female and male. Is that possible?

Following code will result in meth object to be used in MDR analysis. Is there a way to separate samples after I have meth? so that I can find the DMR for each male and female?


    obj=methRead(location=file.list,sample.id, assembly="hg38", treatment= treatment, context="CpG")meth=unite(filtered.obj, min.per.group=1L, destrand=FALSE)

    filtered.obj=filterByCoverage(obj,lo.count=10,lo.perc=NULL, hi.count=NULL,hi.perc=99.9)

    normalizeCoverage(filtered.obj,method="median") 

    meth=unite(filtered.obj)

DMR

myDiff=calculateDiffMeth(meth,mc.cores=2)
rrbs dmr methylkit • 397 views
ADD COMMENTlink modified 12 months ago • written 12 months ago by maria2019100
1

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

ADD REPLYlink written 12 months ago by _r_am31k
2
gravatar for jomo018
12 months ago by
jomo018610
jomo018610 wrote:

I haven't actually tried your exact workflow however I believe you can use reorganize to select samples for downstream. The command should be inserted in your case between unite and calculateDiffMeth.

ADD COMMENTlink written 12 months ago by jomo018610

Thank you!!! I just checked it. I believe that is what I needed.

ADD REPLYlink written 12 months ago by maria2019100

I have moved jomo018's comment to an answer. If it solved your problem, please click the green check mark to accept this answer.

ADD REPLYlink written 12 months ago by _r_am31k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1192 users visited in the last hour