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.

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.

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)