calcOpenSignal {GenomicDistributions} | R Documentation

## The function calcOpenSignal takes the input BED file(s) in form of GRanges or GRangesList object, overlaps it with all defined open chromatin regions across cell types and returns a matrix, where each row is the input genomic region (if overlap was found), each column is a cell type, and the value is a normalized ATAC-seq signal.

### Description

The function calcOpenSignal takes the input BED file(s) in form of GRanges or GRangesList object, overlaps it with all defined open chromatin regions across cell types and returns a matrix, where each row is the input genomic region (if overlap was found), each column is a cell type, and the value is a normalized ATAC-seq signal.

### Usage

    calcOpenSignal(query, cellMatrix)

### Arguments

`query` | Genomic regions to be analyzed. Can be GRanges or GRangesList object.
`cellMatrix` | Matrix with open chromatin signal values, rows are genomic regions, columns are cell types. First column contains information about the genomic region in following form: chr_start_end. Can be either data.frame or data.table object.

### Value

A list with named components: signalMatrix - data.table with cell specific open chromatin signal values for query regions matrixStats - data.frame containing boxplot stats for individual cell type

### Examples

    openRegionSummary = calcOpenSignal(vistaEnhancers, exampleOpenSignalMatrix_hg19)

[Package GenomicDistributions version 1.2.0 Index]