compute_ploidy: Function to compute ploidy from a beta table.

In CLONETv2: Clonality Estimates in Tumor

Description

This function takes the beta table of a tumor sample and returns its ploidy.

Usage

compute_ploidy(beta_table, max_homo_dels_fraction = 0.01,
  beta_limit_for_neutral_reads = 0.9, min_coverage = 20,
  min_required_snps = 10, library_type = "WES", n_digits = 3,
  n_cores = 1)

Arguments

beta_table	data.frame formatted as the output of function compute_beta_table
max_homo_dels_fraction	estimated maximum proportion of genomic segments corresponding to an homozygous deletion (default=0.01)
beta_limit_for_neutral_reads	minimum beta value of a segment valid for computing ploidy (default=0.90)
min_coverage	minimum coverage of a segment valid for computing ploidy (default=20)
min_required_snps	minimum number of informative snps in a segment valid for computing ploidy (default=10)
library_type	WES, WGS (default=WES)
n_digits	number of digits in the output table (default=3)
n_cores	number of available cores for computation (default=1)

Value

A data.frame with two columns: sample that corresponds to column sample of the input beta_table, and ploidy computed

Author(s)

Davide Prandi

Examples

## Compute ploidy table with default parameters
pl_table_toy <- compute_ploidy(bt_toy)

CLONETv2 documentation built on Oct. 14, 2021, 1:07 a.m.