Get CN States.

Get a copy number matrix for all samples based on segmented data in the database. This function is deprecated and has been replaced by GAMBLR.utils::segmented_data_to_cn_matrix and GAMBLR.results::get_cn_segments

Usage

get_cn_states()

Value

Copy number matrix with sample_id as rows and regions as columns.

Details

This function returns CN states for the specified regions using the CN data from GAMBLR.results and (optionally) assumes regions with no data are diploid. For how to determine/specify the coordinates of each region, refer to the parameter descriptions and examples.

Examples

if (FALSE) { # \dontrun{
  get_cnv_and_ssm_status()
} # }