Chop Genomic Segments into Fixed-Size Genomic Bins

Splits variable-length copy number segments into fixed-size genomic bins (windows) of a specified width (e.g., 500 Kb).

Usage

segs_to_reads(
  segs_df,
  bin_size = 5e+05,
  genome_version = c("hg19", "hg38"),
  return_type = c("tibble", "granges"),
  seg_start_col = "start",
  seg_end_col = "end",
  sample_id_col = "cell_id",
  state_col = "state",
  other_meta_cols = c(),
  chrom_col = "chr"
)

Arguments

segs_df

A data.frame or tibble containing genomic segments with start, end, and chromosome name columns.

bin_size

Numeric. The width of the genomic windows in base pairs. Defaults to 5e5 (500 Kb).

genome_version

Character. The assembly build to use for creating genomic windows. Must be one of "hg19" or "hg38".

return_type

Character. The format of the returned object. Must be one of "granges" or "tibble". Defaults to "tibble".

seg_start_col

Character. The name of the column in segs_df representing segment start coordinates. Defaults to "start".

seg_end_col

Character. The name of the column in segs_df representing segment end coordinates. Defaults to "end".

sample_id_col

Character. The name of the column in segs_df identifying the sample or cell. Defaults to "cell_id".

state_col

Character. The name of the column in segs_df representing the copy number state. Defaults to "state".

other_meta_cols

Character vector. Optional additional metadata column names in segs_df to carry over to the output. Defaults to an empty vector.

chrom_col

Character. The name of the column in segs_df representing chromosomes. Defaults to "chr".

Value

Depending on return_type:

• "granges": A GRanges object containing the chopped bins with associated metadata columns.

• "tibble": A tibble version of the GRanges object, with the chromosome column renamed back to chrom_col.

In both formats, the output retains the original segment start and end positions in the seg_start and seg_end metadata columns.