exampleOpenSignalMatrix_hg19: A dataset containing a subset of open chromatin regions...

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

A dataset containing a subset of open chromatin regions across all cell types defined by ENCODE for Homo Sapiens hg19

Description

Preparation steps:

1. made a universe of regions by merging regions across cell types defined as opened in ENCODE

2. took bigwig files from ENCODE for individual cell types, merged replicates, filtered out blacklisted sites

3. evaluated the signal above regions defined by previous step

4. performed quantile normalization

5. subsetted it

Usage

data(exampleOpenSignalMatrix_hg19)

Format

data.frame, rows represent whole selection of open chromatin regions across all cell types defined by ENCODE, columns are individual cell types and values are normalized open chromatin signal values.

Source

http://big.databio.org/open_chromatin_matrix/openSignalMatrix_hg19_quantileNormalized_round4.txt.gz

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.