dsa: A DSArray object storing the counts of methylation patterns...

In PeteHaitch/DSArray: Compressed In-Memory Representation of 3-Dimensional Arrays That Contain Many Duplicate Slices

Description

A dataset containing counts of methylation patterns at 1,000,000 randomly sampled CpG 4-tuples from 17 samples. Whilst these data are extracted from real biological experiments, they are for illustrative purposes only and are fairly useless without the associated genomic co-ordinates and other metadata.

Usage

dsa

Format

A DSArray object with 1,000,000 rows (tuples), 17 columns (samples), and 16 slices (possible methylation patterns):

Rows

rows have been deidentified by removing the genomic co-ordinates

Columns

sample names. Please consult the original publications for sample descriptions

Slices

The type of methylation pattern, e.g., MMMM means methylated at all 4 CpGs in the 4-tuple

Details

The DSArray representation of the data use 70 Mb of memory compared to 1 Gb for the array representation.

Source

Data originally published in:

• Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462,315-322 (2009)

• Lister, R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 471, 68-73 (2011)

Data re-analysed by Peter Hickey using methtuple (https://github.com/PeteHaitch/methtuple) to extract the methylation patterns at 4-tuples.

PeteHaitch/DSArray documentation built on May 8, 2019, 1:30 a.m.