The function calcSummarySignal takes the input BED file(s) in form of GRanges or GRangesList object, overlaps it with all defined open chromatin regions across conditions (e.g. cell types) and returns a matrix, where each row is the input genomic region (if overlap was found), each column is a condition, and the value is a meam signal from regions where overlap was found.

The function calcSummarySignal takes the input BED file(s) in form of GRanges or GRangesList object, overlaps it with all defined open chromatin regions across conditions (e.g. cell types) and returns a matrix, where each row is the input genomic region (if overlap was found), each column is a condition, and the value is a meam signal from regions where overlap was found.

calcSummarySignal(query, signalMatrix)

Arguments

query

Genomic regions to be analyzed. Can be GRanges or GRangesList object.

signalMatrix

Matrix with signal values in predfined regions, where rows are predefined genomic regions, columns are conditions (e.g. cell types in which the signal was measured). 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: signalSummaryMatrix - data.table with cell specific open chromatin signal values for query regions matrixStats - data.frame containing boxplot stats for individual cell type

Examples

signalSummaryList = calcSummarySignal(vistaEnhancers, exampleOpenSignalMatrix_hg19)