DMRcate results file ordered by genomic location and not Stouffer p-val?
1
0
Entering edit mode
Ellen O • 0
@ellen-o-12679
Last seen 13 months ago
Stellenbosch University, South Africa

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
DMRcate dmrcate methylation • 715 views
ADD COMMENT
1
Entering edit mode
Tim Peters ▴ 120
@tim-peters-7579
Last seen 6 weeks ago
Australia

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

ADD COMMENT
0
Entering edit mode

Thanks very much, Tim!

ADD REPLY

Login before adding your answer.

Traffic: 488 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