openSignalMatrix_hg19: A dataset containing open chromatin regions across all cell...

In databio/GenomicDistributionsData: Reference data for GenomicDistributions package

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

Usage

openSignalMatrix_hg19(metadata=FALSE)

Arguments

metadata

logical value indicating whether only metadata should be returned or if the resource should be loaded

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.

Value

A data.frame with hg19 open chromatin regions.

Source

http://big.databio.org/open_chromatin_matrix/openSignalMatrix_hg19_percentile99_01_quantNormalized_round4d.txt.gz

Examples

## Not run: 
hg19OpenSignal = openSignalMatrix_hg19()

## End(Not run)

databio/GenomicDistributionsData documentation built on Jan. 29, 2022, 9:31 p.m.