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extract the legths of chains of osscilating copy number segments

Source: R/cn_features.R
extract_oscillations.Rd

Osscilating segments of copy numbers take from of N-M-N, e.g., 3-4-3. The length of these chains reflects the number of oscillations. Chains are evaluated in 3-segment intervals (the minimum required to recognize an oscillation). Chromosomse with < 3 segments cannot have oscillations, and will receive a 0.

Usage

extract_oscillations(
  segs_df,
  middle_bound = 2,
  ends_bound = 0,
  sample_col = "cell_id",
  chrom_col = "chr",
  cn_col = "state",
  return = c("values", "counts")
)

Arguments

segs_df

dataframe. Copy number segments for samples.

middle_bound

integer. How many copy number values away the middle segment can be from the end segments to count as an oscillation. Default 2 (e.g., 3-4-3 and 3-5-3 both count as oscillations, but 3-7-3 would not).

ends_bound

integer. How many CN values apart the two ends of a 3-segment set are allow to be to count as an oscillation. Default is 0, i.e., they must be the same copy number.

sample_col

string. Name of column with cell/sample names

chrom_col

string. Name of column with chromosome names

cn_col

string. Name of column with segment copy number states.

return

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

Value

dataframe. sample IDs and observed chain lengths.

Details

Chromosomes are evaluated in 3-segments sliding windows, with a window receiving a 1 if the 3-set is an oscillation, and a 0 if not. Adjacent oscillation sets are summed, non-osscilating sets are left as 0.

Examples of Chain : length

  • 2-3-4: 0

  • 3-4-3 : 1

  • 3-4-3-4: 2

  • 3-4-3-2: 1 0 (3-4-3 is a chain, 4-3-2 is not)

  • 2-3-4-5: 0 0

An early paper arguing for the use of oscillations to detect chromothripsis outlined that oscillations should be within 1 or 2 CN values. Using N-M-N notation from above, this would mean that Ns should be the same value and M would be within 1 or 2 copy values of N. Some pubilications relax these constraints, and for example allow M to be any value other than N. This means that 3-300-3 is counted as an oscillation by several publications. Granted, this is an oscillation, but not likely to be one indicative of chromothripsis.

Others allow some flexiblity in the matching of the first and second N, allowing them to be within some margin of difference. Componding these two things leads to fairly extreme senarios, with some methods allowing chains like 5-300-6 to count as an oscillation.

These behaviours can be replicated here, but isn't recommended. By default, Ns must match exactly, and M must be within 2 CNs.

Optionally can summarize in counts of pre-defined categories of:

Oscillation chains of length: 0, 1-3, 4-9, 10+