check_ploidy_and_admixture: Function to compute ploidy from a beta table.
In CLONETv2: Clonality Estimates in Tumor

Description Usage Arguments Value Author(s) Examples

View source: R/CLONETv2_check_ploidy_and_admixture.R

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

1	check_ploidy_and_admixture(beta_table, ploidy_table, admixture_table)

`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`

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.

Davide Prandi

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## 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)