create_score_matrix {Onassis} | R Documentation |
createScoreMatrix
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.
create_score_matrix(ref_granges, granges_list)
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 |
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.
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)