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calculate sample ploidy with a weighted CN mean

Source: R/ploidy.R
weighted_ploidy.Rd

CN is first weighted by the length of its segment, a weighted mean of these segments for each chromosome is made, then the mean across all chrosomomes is made for each sample.

Usage

weighted_ploidy(
  cn_df,
  sample_col = "cell_id",
  start_col = "start",
  end_col = "end",
  cn_col = "state",
  chrom_col = "chr"
)

Arguments

cn_df

dataframe input of segmented (or not) sample copy numbers

sample_col

string column name identifying samples

start_col

string column name identifying start of segments

end_col

string column name identifying end of segments

cn_col

string column name for copy number states

chrom_col

string column name for chromosomes

Value

tibble of per-sample ploidy estimates

Details

In this way, the CN contribution to the ploidy is based on it's length, and each chromosome contributes equally to the overall sample ploidy.