Question: BS-seq differential methylation analysis using continuous variable
0
gravatar for enricoferrero
4.0 years ago by
enricoferrero570
Switzerland
enricoferrero570 wrote:

I want to detect differentially methylated regions (DMRs) on a whole-genome bisulfite sequencing (BS-seq) dataset. 

However, instead of having two groups to compare, I'm working with a clinical parameter that is a continuous variable and would like to identify changes for unit of increase of my clinical parameter.

Software packages for RNA-seq analysis such as DESeq2 allow that by simply including the continuous variable in the model formula.

How can I perform a differential methylation analysys of BS-seq data using a continuous variable? What Bioconductor package(s) can I use?

Thanks!

bsseq deseq2 biseq methylation dmr • 1.3k views
ADD COMMENTlink modified 4.0 years ago by Kasper Daniel Hansen6.4k • written 4.0 years ago by enricoferrero570
Answer: BS-seq differential methylation analysis using continuous variable
1
gravatar for Kasper Daniel Hansen
4.0 years ago by
United States
Kasper Daniel Hansen6.4k wrote:
I'm currently working on adding this capability to bsseq. It's not ready yet, but might be available soon. You should think about which scale you want to do the analysis on, and whether it makes sense, given the bounded nature of methylation. Best, Kasper On Thu, Oct 22, 2015 at 9:44 AM, enrico16 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User enrico16 <https: support.bioconductor.org="" u="" 6037=""/> wrote Question: > BS-seq differential methylation analysis using continuous variable > <https: support.bioconductor.org="" p="" 73691=""/>: > > I want to detect differentially methylated regions (DMRs) on a > whole-genome bisulfite sequencing (BS-seq) dataset. > > However, instead of having two groups to compare, I'm working with a > clinical parameter that is a continuous variable and would like to identify > changes for unit of increase of my clinical parameter. > > Software packages for RNA-seq analysis such as DESeq2 allow that by simply > including the continuous variable in the model formula. > > *How can I perform a differential methylation analysys of BS-seq data > using a continuous variable? What Bioconductor package(s) can I use?* > > Thanks! > > ------------------------------ > > Post tags: dmr, methylation, deseq2, bsseq, biseq > > You may reply via email or visit BS-seq differential methylation analysis using continuous variable >
ADD COMMENTlink written 4.0 years ago by Kasper Daniel Hansen6.4k

Thank you. That's great to hear and I look forward to it.

Do you know of any other package that allows to do that?

ADD REPLYlink written 4.0 years ago by enricoferrero570
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