In LeireAbarrategui/epimutacionsData: Data for epimutacions package

knitr::opts_chunk$set(echo = TRUE)

Introduction

The epimutacionsData package is a repository of datasets for the epimutacions package. It includes 2 datasets to use as an example:

• Reference panel: DNA methylation profiles of 24 whole cord blood samples from healthy children born via caesarian (GEO: GSE127824)
• Case and control samples: DNA methylation profiling of whole blood samples in healthy children (GSE104812). CHARGE and Kabuki syndromes whole blood samples DNA methylation profiles (GEO: GSE97362).
• Candidate regions: Regions in Illumina 450K array which are candidate to be epimutations.

Installation

The following code explains how to access to the data:

library(ExperimentHub)
eh <- ExperimentHub()
query(eh, c("epimutacionsData"))

Candidate epimutations

In Illumina 450K array [@reproducibilityinfinium], probes are unequally distributed along the genome, limiting the number of regions that can fulfil the requirements to be considered an epimutation. So, we have computed a dataset containing the regions that are candidates to become an epimutation.

To define the candidate epimutations, we relied on the clustering from bumphunter [@jaffe2012bump]. We defined a primary dataset with all the CpGs from the Illumina 450K array. Then, we run bumphunter and selected those regions with at least 3 CpGs. As a result, we found 40408 candidate epimutations which are available in the candRegsGR dataset.

candRegsGR <- eh[["EH6692"]]

Example datasets

Reference panel

The package includes an RGChannelSet class reference panel (reference_panel) which contains 22 whole cord blood samples from healthy children born via caesarian from the GSE127824 cohort [@gervin2019systematic].

The reference panel can be found in EH6691 record of the eh object:

reference_panel <- eh[["EH6691"]]

Control and case samples

The methy dataset includes 51 DNA methylation profiling of whole blood samples. 48 controls from GSE104812 [@shi2018dna] cohort and 3 cases from GSE97362 [@butcher2017charge]. it is a GenomicRatioSet class object.

methy <- eh[["EH6690"]]

IDAT files

The IDAT files contain raw microarray intensities of 4 case samples from GSE131350 cohort. The files are located on the external data of epimutacionsData package:

library(minfi)
baseDir <- system.file("extdata", package = "epimutacionsData")
targets <- read.metharray.sheet(baseDir)

sessionInfo()

sessionInfo()

References

LeireAbarrategui/epimutacionsData documentation built on April 14, 2022, 1:42 a.m.