Mark if CN states are gains or losses relative to cell ploidy

CNs > 2 are not necessarily amplifications, and CNs < 2 are not necessarily the only states of losses. Ploidy of samples may not be diploid. This function will give you an idea if the CN you see is a gain or loss relative to the ploidy of a sample. For example, if the sample has a ploidy of 4, then a CN of 3 is a loss.

Usage

mark_cn_relative_to_ploidy(
  in_df,
  df_type = c("reads", "segs"),
  sample_col = "cell_id",
  ...
)

Arguments

in_df

dataframe of CN states.

df_type

string. "reads" (default) or "segs" for CN segments, which will internally converted to bin based for mode calculation. reads in order to infer mode ploidy.

sample_col

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

Value

input dataframe, with new columns of information.

Details

Ploidy is inferred by mode CN state using mode_ploidy() and states > ploidy are marked as gains, states < ploidy losses, and states matching ploidy as matched.