create_score_matrix {Onassis} | R Documentation

## `createScoreMatrix`

### Description

This functions allows the creation of a score matrix for genomic regions overlapping the genomic regions provided as reference (e.g. promoter regions). Each entry of the matrix corresponds to 1 if the sample represented on the column overlaps the genomic interval represented on the row.

### Usage

    create_score_matrix(ref_granges, granges_list)

### Arguments

`ref_granges` | An object of type GRanges to be considered as the reference GRanges
`granges_list` | A list of GRanges, one for each sample, to be mapped on the reference granges

### Value

A logical score matrix where the number of rows corresponds to the number of different genomic intervals in the ref_granges object and each column is associated to a Grange in the granges_list. Score(i, j) is set to 1 if the j-th sample has a interval overlapping the one in the i-th row of the reference GRanges.

### Examples

    granges <- readRDS(system.file('extdata', 'sample_granges.rds', package='Onassis'))
    ref_granges <- granges[[1]]

    for(i in 2:length(granges)) {
     ref_granges <- GenomicRanges::union(ref_granges, granges[[i]])
    }
    score_mat <- create_score_matrix(ref_granges, granges)

[Package Onassis version 1.2.7 Index]