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.
multisample_init(
cnaqc_objs,
QC_filter = TRUE,
keep_original = TRUE,
discard_private = FALSE
)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.
logical. Indicates whether to filter or not for QC-passing mutations (NB: must have performed the peak analysis before).
Default is TRUE.
logical. Indicates whether to keep or not original CNAqc objects, default is TRUE
logical. Indicates whether to keep or not mutations falling on private segments, default is FALSE.
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.
if (FALSE) { # \dontrun{
multisamples = CNAqc::multisample_init(cnaqc_objs = CNAqc_samples,
QC_filter = TRUE,
keep_original = FALSE,
discard_private = FALSE)
multisamples
} # }