compute_scna_clonality_table: Function to compute clonality of somatic copy number data
In CLONETv2: Clonality Estimates in Tumor

Description Usage Arguments Value Author(s) Examples

View source: R/CLONETv2_compute_scna_clonality_table.R

This function takes the beta table of a tumor sample together with the associated ploidy and admixtures tables and computes the clonality of each segment in the beta table.

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compute_scna_clonality_table(beta_table, ploidy_table, admixture_table,
  error_tb = error_table, clonality_threshold = 0.85,
  beta_threshold = 0.9, n_digits = 3, n_cores = 1, debug = F)

`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`
`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)
`clonality_threshold`	threshold to discretize continuous clonality value (default=0.85)
`beta_threshold`	threshold on beta value to determine clonality direction (default=0.90)
`n_digits`	number of digits in the output table (default=3)
`n_cores`	number of cores (default=1)
`debug`	return extra columns for debugging (default=F)

A data.frame that extends input beta_table with columns

clonality: estimated fraction of tumor cell with log2 copy number
clonality.min: minum estimated fraction of tumor cell with log2 copy number
clonality.max: minum estimated fraction of tumor cell with log2 copy number
clonality.status: discretized clonality status into five values: clonal, large majority of the tumor cells has the same copy number; subclonal, not all the tumor cells has the same copy number; not.analysed, is is not possible to determine clonality; uncertain.clonal and uncertain.subclonal correspond respectively to clonal and subclonal populations but with less reliable clonality estimate

Davide Prandi

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## Compute clonality table with default parameters
scna_clonality_table_toy <- compute_scna_clonality_table(beta_table = bt_toy,
  ploidy_table = pl_table_toy, admixture_table = adm_table_toy)