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Extract CN features following Wu et al

Source: R/cn_features.R
extract_wu_features.Rd

This function extracts copy number features in the style of the paper:

Usage

extract_wu_features(
  segs_df,
  sample_col = "cell_id",
  state_bin_max = 5,
  bin_breaks = NA,
  annotate_input = FALSE,
  return_matrix = FALSE,
  ...
)

Arguments

segs_df

dataframe. CN segments

sample_col

string. Name of the column with cell_id/other sample name

state_bin_max

int. Maximum CN to consider for bins. All CNs of this value and higher are grouped together. Default of 5 follows paper.

bin_breaks

floats, how to break up segment sizes. Bins will be one more than breaks. Defaults follow paper. Default is < 5Mb, 5–10Mb, > 10Mb specified as c(5e6, 10e6 + 1). Internally, base::cut() is used, so 2 splits produces 3 bins.

annotate_input

boolean. return input dataframe annotating each segment with the feature categories it falls into.

return_matrix

boolean. Return a cell-by-feature matrix of counts.

...

can pass change_split_val to alter critical value for AA/BB split

Value

default return is a tibble of feature counts for each cell id.

Details

Wu et al. 2025. Single-cell copy number alteration signature analysis reveals masked patterns and potential biomarkers for cancer. bioRxiv.

https://www.biorxiv.org/content/10.1101/2025.03.02.641098v1

They employ 4 base features, that they cross for 90 categories:

  1. CN states: 5 bins, 0-1, 2, 3, 4, 5+

  2. segment size: 3 bins, <5 MB, 5-10Mb, 10Mb,

  3. segment shape: 3 bins, LL (low left, low right segment), HH (high left, high right segment), OT (other)

  4. segment change: 2 bins: AA (difference between surrounding segments <= some critical value), or BB

Some issues:

  • whole chromosome amplifications/losses not captured

  • chromosomes need to have at least 3 changes to be truly reflected in these categories. Those with fewer are backfilled based on hardcoded rules

  • for segment change, the paper says they considered changes > 2 as BB, but in their actual code is set to 1. This function follows their code, but can be altered.