Question: DMR calling for EWAS meta-analysis
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gravatar for mark.ziemann
4 weeks ago by
mark.ziemann1.3k
Australia/Mebourne/Geelong/Deakin
mark.ziemann1.3k wrote:

Hi Biostars,

I'm looking for a package/tool that can perform DMR calling of Infinium array data after meta-analysis. All the packages I've seen so far (eg:DMRcate and bumphunter) require the original matrices of m- or beta-values which won't work for us.

We tried combp from the ENmix package but that gave an error during execution so we are lookig for more options.

We posted the combp error to a different forum https://support.bioconductor.org/p/p132476/


> str(nat_vs_art_combp_filter)

'data.frame':   45151 obs. of  5 variables:

 $ V1: chr  "chr1" "chr1" "chr1" "chr1" ...

 $ V2: int  184943512 39957206 229694784 38273761 95700082 155532716 115053835 27114420 11865920 39457099 ...

 $ V3: int  184943512 39957206 229694784 38273761 95700082 155532716 115053835 27114420 11865920 39457099 ...

 $ V4: num  9.09e-22 3.69e-20 7.06e-20 1.95e-19 4.33e-19 ...

 $ V5: Factor w/ 455828 levels "cg00000029","cg00000108",..: 413831 287383 207196 397045 424258 339026 277278 303634 442510 414728 ...

> combp(nat_vs_art_combp_filter,dist.cutoff=1000,bin.size=310,seed=0.5, region_plot=TRUE,mht_plot=TRUE,nCores=10)

Error in if (any(p.stouffer > 0.05)) { : 

  missing value where TRUE/FALSE needed


Thanks!

ADD COMMENTlink modified 20 days ago by Biostar ♦♦ 20 • written 4 weeks ago by mark.ziemann1.3k
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