Functions for loading the http://www.ariesepigenomics.org.uk/ DNA methylation profiles.
The Accessible Resource for Integrated Epigenomic Studies (ARIES) is a BBSRC-funded resource of epigenomic information on a range of human tissues, including DNA methylation data on peripheral blood at multiple time points across the lifecourse.
Caroline L Relton, Tom Gaunt, Wendy McArdle, Karen Ho, Aparna Duggirala, Hashem Shihab, Geoff Woodward, Oliver Lyttleton, David M Evans, Wolf Reik, Yu-Lee Paul, Gabriella Ficz, Susan E Ozanne, Anil Wipat, Keith Flanagan, Allyson Lister, Bastiaan T Heijmans, Susan M Ring, and George Davey Smith. Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES) Int. J. Epidemiol. (2015) 44 (4): 1181-1190
http://www.ariesepigenomics.org.uk/
Access to the ARIES dataset can be obtained by submitting a project proposal to the Avon Longitudinal Study of Parents and Children (ALSPAC) executive committee (http://www.bristol.ac.uk/alspac/researchers/access/).
Once you have a copy of the dataset, this R package can be used to load the ARIES dataset in R.
Install the devtools package if it is not already installed:
install.packages("devtools")
Load devtools and then install aries.
library(devtools)
install_github("MRCIEU/aries")
The following example shows how to load the methylation profiles for blood samples collected around age 15.
library(aries)
aries.dir <- "path/to/aries"
aries <- aries.select(aries.dir, time.point="15up")
aries$meth <- aries.methylation(aries)
A more complete example including a basic EWAS is also available.
Note that, by default, DNA methylation data will have all
probe intensities with detection p-values > 0.01 will appear as missing values (i.e. NA).
To include these values, set no.missing to TRUE, e.g.
aries$meth <- aries.methylation(aries,no.missing=T)
| Illumina 450k | Illumina EPIC | Description | |
|---|---|---|---|
| cord | 914 | 0 | Study child cord blood |
| c43m | 85 | 0 | Study child age 3.5y |
| c61m | 34 | 0 | Study child age 5y |
| F7 | 978 | 0 | Study child age 7y |
| F9 | 374 | 0 | Study child age 9y |
| 15up | 981 | 1920 | Study child age 15-17y |
| F24 | 0 | 828 | Study child age 24y |
| antenatal | 987 | 0 | Mothers during the study child pregnancy |
| FOM | 992 | 0 | Mothers approximately 18 years after study pregnancy |
| FOF | 588 | 0 | Fathers approximately 18 years after study pregnancy |
These numbers can be obtained from the data using following code:
library(aries)
aries.dir <- "path/to/aries"
info <- aries.info(path="")
with(info$common$samples, table(time_point,chip))
Blood cell counts were estimated using published DNA methylation references using the meffil R package:
https://github.com/perishky/meffil/wiki/Estimating-cellular-composition