BS-seq differential methylation analysis using continuous variable
1
0
Entering edit mode
enricoferrero ▴ 570
@enricoferrero-6037
Last seen 6 months ago
Switzerland

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!

dmr methylation deseq2 bsseq biseq • 1.5k views
ADD COMMENT
1
Entering edit mode
@kasper-daniel-hansen-2979
Last seen 20 days ago
United States
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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 830 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6