CLONETv2 (version 2.2.1)

compute_dna_admixture: Function to compute DNA admixture of a tumor sample from the associatd beta table and ploidy table

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

Examples

# NOT RUN {
## Compute admixture table with default parameters
adm_table_toy <- compute_dna_admixture(beta_table = bt_toy, ploidy_table = pl_table_toy)

# }