exampleHummingbird: Sample dataset

In hummingbird: Bayesian Hidden Markov Model for the detection of differentially methylated regions

Description

Example of input data for the hummingbird package.

The sample dataset is partial data of chromosome 29 in the large offspring syndrome (LOS) study described in Chen Z. et al (2017).

Usage

data("exampleHummingbird")

Format

experimentSEControl

A SummarizedExperiment object containing the input data for the control group: The two assays: normM, normUM and the CpG position information: pos.

experimentSECase

A SummarizedExperiment object containing the input data for the case group: The two assays: abnormM, abnormUM and the CpG position information: pos.

normM

A matrix containing the methylated read count data of the control group. Each column of the matrix represents a replicate and each row represents a CpG position.

normUM

A matrix containing the unmethylated read count data of the control group. Each column of the matrix represents a replicate and each row represents a CpG position.

abnormM

A matrix containing the methylated read count data of the case group. Each column of the matrix represents a replicate and each row represents a CpG position.

abnormUM

A matrix containing the unmethylated read count data of case group. Each column of the matrix represents a replicate and each row represents a CpG position.

pos

The CpG positions.

Source

Chen et al. (2017) Global misregulation of genes largely uncoupled to DNA methylome epimutations characterizes a congenital overgrowth syndrome. Scientific Reports 7, 12667

The raw FASTQ files of the WGBS experiment from this study are publicly available at Gene Expression Omnibus (GEO) database with accession no. GSE93775.

Examples

library(SummarizedExperiment)
data(exampleHummingbird)

hummingbird documentation built on April 18, 2021, 6 p.m.