CLONETv2 (version 2.2.1)

check_ploidy_and_admixture: Function to compute ploidy from a beta table.

Description

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

Usage

check_ploidy_and_admixture(beta_table, ploidy_table, admixture_table)

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

admixture_table

data.frame formatted as the output of function compute_dna_admixture

Value

A ggplot2 plot reporting log2 on the x axis and beta and the y axis. Each dot represents a segment of the input beta_table. Red transparent circles corresponds to expected log2 vs beta position for different allele specific copy number combinations given ploidy and admixture reported in tables ploidy_table and admixture_table, respectively. Labels in the form (cnA, cnB) indicate repsectively the major and minor allele copy number value. Labels above the plot comprises sample name and ploddy/admixture estimates.

Examples

# NOT RUN {
## check ploidy and admixture estimates
check_plot_toy <- check_ploidy_and_admixture(beta_table = bt_toy, ploidy_table = pl_table_toy,
  admixture_table = adm_table_toy)

# }