copy_number_maxima: Obtain maxima in a distribution of relative copy numbers.

In crukci-bioinformatics/rascal: Shiny app and functions for scaling relative copy number data to absolute values

Description

This function obtains peaks in the density for the given set of relative copy numbers.

Usage

copy_number_maxima(
  copy_numbers,
  min_copy_number = 0,
  max_copy_number = 3,
  lower_threshold = 0
)

Arguments

copy_numbers	a numeric vector of absolute copy number values.
min_copy_number	the lower copy number value in the range of values to estimate the density.
max_copy_number	the upper copy number value in the range of values to estimate the density.
lower_threshold	the lower threshold for a maximum as a fraction of the density of the largest maximum.

Value

a data frame with copy number and density columns and a row for each maximum in the distribution.

Examples

data(copy_number)
copy_number <- copy_number[copy_number$sample == "X17222", ]
maxima <- copy_number_maxima(copy_number$segmented, lower_threshold = 0.1)

crukci-bioinformatics/rascal documentation built on Dec. 19, 2021, 6:21 p.m.