View source: R/rebinGenomicInteractions.R
rebinGenomicInteractions | R Documentation |
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.
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. |
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")
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