I am following a published workflow on methylation analysis and am currently looking at differentially methylated regions with dmrcate. My results come back ordered by chromosomal region, but I understand that by default they should be ordered by the Stouffer p-value? I have tried to sort the data by p-value using order() but I can't get it right (I am an R newbie). When I write it to excel and sort it there, it matches up with the results in the paper, so I know that the results are correct, they are just ranked incorrectly in R. Does anyone know why this is happening and how I can change it? Code below (from Maksimovic et al. 2016). Thank you!

myAnnotation <- cpg.annotate(object = mVals, datatype = "array", what = "M", 
                             analysis.type = "differential", design = design, 
                             contrasts = TRUE, cont.matrix = contMatrix, 
                             coef = "naive - rTreg", arraytype = "450K")
DMRs <- dmrcate(myAnnotation, lambda=1000, C=2)
head(DMRs$results)

​What I get:

##                  coord no.cpgs       minfdr    Stouffer  maxbetafc  meanbetafc
## 1 chr1:1149501-1150936       6 5.984538e-56 0.001088019  0.2693474  0.11443808
## 2 chr1:2003577-2004636       9 2.742863e-42 0.762659787  0.3441610  0.09161004
## 3 chr1:2058941-2059086       2 5.902550e-18 0.032585707 -0.2040435 -0.15183179
## 4 chr1:2228160-2229113       4 8.885648e-78 0.038966222 -0.4400900 -0.17788349
## 5 chr1:2516401-2516516       2 1.285306e-17 0.181109097  0.2476914  0.13585802
## 6 chr1:3289798-3289994       3 3.012113e-18 0.057362507  0.1991512  0.10041011

What the authors get:

##                          coord no.cpgs        minfdr     Stouffer  maxbetafc
## 457    chr17:57915665-57918682      12  4.957890e-91 6.639928e-10  0.3982862
## 733   chr3:114012316-114012912       5 1.622885e-180 1.515378e-07  0.5434277
## 469    chr17:74639731-74640078       6  9.516873e-90 1.527961e-07 -0.2528645
## 1069    chrX:49121205-49122718       6  6.753751e-84 2.936984e-07  0.4529088
## 492    chr18:21452730-21453131       7 5.702319e-115 7.674943e-07 -0.3867474
## 186  chr10:135202522-135203200       6  1.465070e-65 7.918224e-07  0.2803157
##      meanbetafc
## 457   0.3131611
## 733   0.4251622
## 469  -0.1951904
## 1069  0.3006242
## 492  -0.2546089
## 186   0.2293419

Hi elleno,

Thanks for picking this up - we rewrote dmrcate() recently to speed it up a bit, but looks like we neglected to reorder the DMRs. I have put the fix in svn and it should propagate to the web within 48 hours, or you can grab the corrected version right now at https://github.com/timpeters82/DMRcate-devel.

Pleasing to see the DMRs themselves are reproduced.

Cheers,
Tim