User: Tim Peters
Tim Peters • 80
- Reputation:
- 80
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- Australia
- Last seen:
- 3 months, 4 weeks ago
- Joined:
- 4 years, 8 months ago
- Email:
- t*******@garvan.org.au
--
Tim Peters, PhD
Bioinformatics Research Officer | Epigenetics Research Laboratory | Genomics and Epigenetics Division
Garvan Institute of Medical Research
384 Victoria St., Darlinghurst, NSW, Australia 2010
Posts by Tim Peters
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... Hi Anne-Kristin,
Yes I would - at the rate at which you specified the fdr. Although I think summarising the significance of a DMR with one single value can be misleading, the Stouffer value is there to do this to placate the people who want one. I see it as an extra level of control if you're still ...
written 3 months ago by
Tim Peters • 80
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... Hi Ann-Kristin,
> In this case I would expect that at least one of the CpGs would show up on the list of significant DMPs from limma, since I thought at least one CpG within the DMR would have to be individually significant. Is this not the case?
No, this is not necessarily the case. DMRcate do ...
written 4 months ago by
Tim Peters • 80
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... Hi Poojitha,
A bit of digging reveals this is a temporary situation:
https://github.com/Bioconductor/GenomicRanges/blob/master/R/GenomicRanges-class.R#L597-L599
https://support.bioconductor.org/p/109137/
So I guess for the time being you'll need to use a for loop:
constituent.cpgs <- list ...
written 4 months ago by
Tim Peters • 80
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... Hi,
Just like with any epigenetic mark, not all DMRs have an unambiguous gene assignment. This is why I've restricted the gene information to overlapping promoters. If you're interested in finding the nearest genes, I would use a method such as this: https://bioconductor.org/packages/release/bioc/v ...
written 4 months ago by
Tim Peters • 80
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Comment:
C: cpg.annotate model requirements
... You can specify `contrasts=TRUE` and pass a contrasts matrix (as you would in limma) to `cpg.annotate`; this will allow you to fit non-intercept models.
Tim ...
written 4 months ago by
Tim Peters • 80
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... Hi Steven,
This is indeed possible using datatype="sequencing" - please look at the second half of the vignette for a worked example.
Best,
Tim
*Edit* My bad, I hadn't realised that the example included only contained output from DSS::DMLtest, not DSS::DMLtest.multiFactor. If you use output fro ...
written 11 months ago by
Tim Peters • 80
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... This is a problem with your version of zlib, not DMRcate. Looks like you need to update the version of zlib on your machine. This thread may be of help: https://www.biostars.org/p/89217/
Cheers,
Tim
...
written 17 months ago by
Tim Peters • 80
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... The extractRanges() function now appends promoter associations from Gencode/Ensembl instead. I find this annotation more reliable than Illumina's. Have a look at page 4 of the vignette:
https://bioconductor.org/packages/release/bioc/vignettes/DMRcate/inst/doc/DMRcate.pdf
Cheers,
Tim
...
written 17 months ago by
Tim Peters • 80
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Comment:
C: Bumphunting for longitudinal data
... Hi Ash,
Yes, it looks like that will work. The ellipsis argument (...) at the end of cpg.annotate() is matched to extra arguments for limma::lmFit(), so block and correlation will propagate to the linear fitting.
And yes, DMRcate can definitely be used for continuous responses as well. The only ca ...
written 19 months ago by
Tim Peters • 80
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... Hi Ash,
Yes, like James said, you'll need to sacrifice some of your covariates to get your design matrix full rank. Once you have a full rank matrix, you can then pass it to cpg.annotate() along with your coefficient of interest (and optionally contrast matrix), and then the regular workflow will d ...
written 19 months ago by
Tim Peters • 80
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