Question

Taking relatedness among individuals into account in differential methylation analysis?

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elgomez • 0

@elgomez-17056

Last seen 4 weeks ago

United States

Hi all,

I am looking for differentially methylated probes and regions with age in a sample set that includes related individuals.

So far I have been using minfi and ChAMP to analyze my 450K and EPIC array data. I've really enjoyed using both of these excellent packages and am grateful to their developers!

But I am wondering if anyone knows of a way to incorporate relatedness (for example, a relatedness matrix) into the linear model used to identify DMPs or into the bumphunter analysis?

Thank you for any thoughts on this,

EG

methylation minfi ChAMP • 1.3k views

ADD COMMENT • link updated 6.3 years ago by Kasper Daniel Hansen ★ 6.5k • written 6.3 years ago by elgomez • 0

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Um...Sorry that I think ChAMP cannot incorporate relatedness matrix, I have never done project involved with that, thus I did not develop this functionality in ChAMP.

Maybe you can consider minfi?

Best

Yuan Tian

ADD REPLY • link 6.3 years ago Yuan Tian ▴ 290

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Thank you for the reply and suggestion.

ADD REPLY • link 6.3 years ago elgomez • 0

score 0 · Answer 1 · 2018-08-26

At first, I would use "standard" tools from GWAS to do this (not saying this is easy), either on data in the unit interval or the logit transformation. In principle all you need is a mixed effect model where the covariance matrix reflects the relatedness structure. On Sat, Aug 25, 2018 at 12:34 AM eeheberlein [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User eeheberlein <https: support.bioconductor.org="" u="" 17056=""/> wrote Question: > Taking relatedness among individuals into account in differential > methylation analysis? <https: support.bioconductor.org="" p="" 112413=""/>: > > Hi all, > > I am looking for differentially methylated probes and regions with age in > a sample set that includes related individuals. > > So far I have been using minfi and ChAMP to analyze my 450K and EPIC array > data. I've really enjoyed using both of these excellent packages and am > grateful to their developers! > > But I am wondering if anyone knows of a way to incorporate relatedness > (for example, a relatedness matrix) into the linear model used to identify > DMPs or into the bumphunter analysis? > > Thank you for any thoughts on this, > > EG > ------------------------------ > > Post tags: methylation, minfi, ChAMP > > You may reply via email or visit > Taking relatedness among individuals into account in differential methylation analysis? >