ADS_iPSC: 'SimulateMethylomeParam' object for the _ADS-iPSC_ sample.

In PeteHaitch/methsim: An R package to simulate DNA methylation data

Description

A SimulateMethylomeParam object for the ADS-iPSC sample from Lister et al. (2011).

Usage

ADS_iPSC

Format

A SimulateMethylomeParam object.

Source

Data originally published in Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68–73 (2011) http://www.ncbi.nlm.nih.gov/pubmed/21289626 and re-analysed by Peter Hickey as follows.

In brief, aligned sequencing data were downloaded from http://neomorph.salk.edu/ips_methylomes/data.html and converted to BAM format using Python scripts available from https://github.com/PeteHaitch/Lister2BAM. Methylation patterns at m-tuples were extracted using methtuple v1.4.0 (https://github.com/PeteHaitch/methtuple) and processed using MethylationTuples (https://github.com/PeteHaitch/MethylationTuples) and methsim (https://github.com/PeteHaitch/methsim). See my PhD thesis for further details (https://github.com/PeteHaitch/phd_thesis), in particular the Datasets chapter.

PeteHaitch/methsim documentation built on May 8, 2019, 1:32 a.m.