rebinGenomicInteractions {CNVScope}

Assign GenomicInteractions to a predefined series of bins for row and column, corresponding to a genomic matrix.

Description

This function allows the user to assign a set of genomicinteractions to a pre-existing matrix with known dimensions and column/row names. It finds the row/column index of each point and produces a merged dataframe with the original annotation columns that correspond to each bin in the matrix, with appropriate labels & indexes.

Arguments

gint

A GenomicInteractions object needing to be binned.

whole_genome_matrix

A matrix with underscored positions for column and rownames e.g. chr1_1_5000,chr1_5001_10000. If this is provided, it will override rown/column names and GRanges objects.

rownames_gr

A Genomic Ranges object created from the whole genome matrix row names in chr_start_end format, e.g. chr1_1_5000. No effect if whole_genome_mattrix is specified.

colnames_gr

A Genomic Ranges object created from the whole genome matrix column names in chr_start_end format. No effect if whole_genome_mattrix is specified.

rownames_mat

The row names of the whole_genome_matrix in chr_start_end format.

colnames_mat

The column names of the whole_genome_matrix in chr_start_end format.

method

Method to rebin with– can use overlap and nearest methods.Default: nearest.

Examples

foreach::registerDoSEQ()
gint_small_chr1<-importBreakpointBed(breakpoint_fn = system.file("extdata",
"sample_breakpoints_chr1.bed",package = "CNVScope"))
load(system.file("extdata","nbl_result_matrix_sign_small.rda",package = "CNVScope")) 
rebinGenomicInteractions(gint=gint_small_chr1,whole_genome_matrix=NULL,
rownames_gr=underscored_pos_to_GRanges(rownames(nbl_result_matrix_sign_small)),
colnames_gr=underscored_pos_to_GRanges(colnames(nbl_result_matrix_sign_small)),
rownames_mat = rownames(nbl_result_matrix_sign_small),
colnames_mat = colnames(nbl_result_matrix_sign_small),
method="nearest")