compute_dna_admixture: Function to compute DNA admixture of a tumor sample from the...

In CLONETv2: Clonality Estimates in Tumor

Description

This function takes a beta table and the associated ploidy table and computes DNA admixture.

Usage

compute_dna_admixture(beta_table, ploidy_table, min_required_snps = 10,
  min_coverage = 20, error_tb = error_table, library_type = "WES",
  n_digits = 3, n_cores = 1, debug = F)

Arguments

beta_table	data.frame formatted as the output of function compute_beta_table
ploidy_table	data.frame formatted as the output of function compute_ploidy
min_required_snps	minimum number of informative snps in a segment valid for computing ploidy (default=10)
min_coverage	minimum coverage of a segment valid for computing ploidy (default=20)
error_tb	data.frame that reports for each combination of coverage and number informative SNPs the expected estimation error around beta. The data.frame error_tb must contains 3 columns: mean.cov mean coverage n.info.snps number of informative SNPs adm.estimation.error estimated error on computed beta on a segment with coverage mean.cov and n.info.snps informative SNPs Package CLONETv2 have built in error_tb named error_table (default=error_table)
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)
debug	return extra columns for debugging (default=F)

Value

A data.frame with two columns: sample that corresponds to column sample of the input beta_table, and amd that represent the fraction of estimated DNA admixture

Author(s)

Davide Prandi

Examples

## Compute admixture table with default parameters
adm_table_toy <- compute_dna_admixture(beta_table = bt_toy, ploidy_table = pl_table_toy)

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