Count changes of state relative to ploidy.

Marks CN segments as a gain or loss, relative to the mode ploidy of the sample. Internally using mark_cn_relative_to_ploidy. See that function for argument details.

Usage

extract_ploidy_cn_feature(
  segs_df = NA,
  sample_col = "cell_id",
  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

annotate_input

boolean. return input dataframe annotating each

return_matrix

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

Value

tibble/dataframe of counts