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extract copy state values.

Source: R/cn_features.R
extract_cn.Rd

This function is really only here to offer the counting in pre-set categories, and provide alignment with other feature extraction types. It is mostly a pointless function and you should probably do this yourself.

Usage

extract_cn(
  segs_df,
  sample_col = "cell_id",
  state_col = "state",
  return = c("values", "counts")
)

Arguments

segs_df

dataframe. copy number segments for samples.

sample_col

string. Name of column with CN state values

return

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

Details

Also, it is a question if copy state should even be used in signature fitting, as this can occassionally lead to the same process being artifically split by ploidy of samples. See Drews et al. for a discussion of this idea.

Predefined categories for summarizing counts are: CN = 1, 2, 3, 4, 5, 6+