HMM_CpG_islands.hg38: Hidden Markov Model (HMM) based CpG island boundaries for...

In trichelab/h5testR: Tests for HDF5-backed DNAme, RNAseq, and MultiAssayExperiment objects

Description

In inst/extdata/HMM_CpG_Islands.R you can see how these were constructed. All of the island models are provided by Dr. Hao Wu of Emory University. The makeCGI software provided by Dr. Wu can be used to generate new models.

Usage

HMM_CpG_islands.hg38

Format

A GRanges object with one metadata column (obsExp, observed/expected)

seqnames

the chromosome the island is on

ranges

an IRanges object with the start and end coordinates

strand

the strand the island is on (all islands are unstranded)

obsExp

observed over expected CpG density across this island

Details

hgXX datasets are for human genome assemblies (hg38 and hg19). (Note that hg19 is equivalent to GRCh37 and hg38 is equivalent to GRCh38.)

mmXX datasets are for mouse genome assemblies (mm10 and mm9). (Note that mm10 is equivalent to GRCm37 and mm9 is equivalent to GRCm37.)

The HMM island paper: https://doi.org/10.1093/biostatistics/kxq005 The citation: Wu et al., Redefining CpG islands using hidden Markov models, Biostatistics, Volume 11, Issue 3, July 2010, pages 499-514.

Source

http://www.haowulab.org/software/makeCGI/

See Also

http://www.haowulab.org/software/makeCGI/

trichelab/h5testR documentation built on July 12, 2020, 5:18 p.m.