multisample_init: Create multisample segmentation
In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

multisample_init

R Documentation

Create multisample segmentation

Description

Creates a mCNAqc object starting from a named list of CNAqc objects on which the quality control has already been performed individually (ie: multiple samples coming from the same patient). Breakpoints from the original CNAqc objects are used to define new breakpoints (and then segments) common across all the samples; in the resulting object, the mutations are remapped on the newly defined segments. The new m_CNAqc object can be used to perform new a quality control analysis with the different segmentation.

Usage

multisample_init(
  cnaqc_objs,
  QC_filter = TRUE,
  keep_original = TRUE,
  discard_private = FALSE
)

Arguments

`cnaqc_objs`	named list of CNAqc objects, one per sample (each element must include at least "mutations", "cna", "reference" and "purity"). Names of the list must correspond to sample_id.
`QC_filter`	logical. Indicates whether to filter or not for QC-passing mutations (NB: must have performed the peak analysis before). Default is `TRUE`.
`keep_original`	logical. Indicates whether to keep or not original CNAqc objects, default is `TRUE`
`discard_private`	logical. Indicates whether to keep or not mutations falling on private segments, default is `FALSE`.

Value

a mCNAqc object, structured as follows: - 'cnaqc_obj_new_segmentation' = list of CNAqc objects for all the samples created using the new segmentation; - 'original_cnaqc_objc' = original CNAqc object, only if the argument keep_original is set to TRUE; - 'original_additional_info' = additional information from the original CNAqc objects, such peaks analysis results of CCF estimation. Only if the argument keep_original is set to FALSE; - 'm_cnaqc_stats' = information related to number of mutations and segments before and after the creationn of the mCNAqc object.

Examples

## Not run: 
multisamples = CNAqc::multisample_init(cnaqc_objs = CNAqc_samples, 
                 QC_filter = TRUE, 
                 keep_original = FALSE, 
                 discard_private = FALSE)

multisamples

## End(Not run)

caravagnalab/CNAqc documentation built on Feb. 28, 2025, 12:08 p.m.