extracting counts of breakpoints per user-defined scope

Counting the number of breakpoints (i.e., transitions between copy number segments) per arm or per window (typically 10Mb).

Usage

extract_breakpoints(
  segs_df,
  scope = c("windows", "arms"),
  genome_version = c("hg19", "hg38"),
  window_size = 1e+07,
  sample_col = "cell_id",
  chrom_col = "chr",
  return = c("values", "counts")
)

Arguments

segs_df

dataframe. Copy number segments for samples

scope

string. "windows" (default) or "arms", i.e., what to target for counting

genome_version

string. "hg19" (default) or "hg38"

window_size

integer. How big of a window to use, if extracting counts per a "windows" scope. Most publications use 10Mb, which is the default (10e6)

sample_col

string. Name of column with cell/sample names

chrom_col

string. Name of column with chromosome names

return

string. "values" (default) or "counts". Values are the observed values for cells, counts are the counts of these values in pre-determined categories.

Value

dataframe. Sample IDs and the observed breakpoint counts per scope.

Details

Optional summarizing in pre-defined categories of:

Arm breakpoints: 0, 1, 2, 3, 4, 5, 6+ Window breakpoints: 0, 1, 2, 3+