cbs
Matrix in which each row corrsponds to a copy number fragment as computed by a circular binary segmentation algorithm. Has to contain at least the following columnnames:
chr - chromosome;
startpos - the first genomic position of a copy number segment;
endpos - the last genomic position of a copy number segment;
CN_Estimate - the copy number estimated for each segment (average value across all subpopulations in the sample).
dm
Matrix in which each row corrsponds to a mutation. Has to contain at least the following columnnames:
chr - the chromosome on which each point mutation is located;
startpos - the genomic position of each mutation;
SP - the subpopulation to which the point mutation has been assigned;
SP_cnv - the subpopulation with copy number variation (CNV) in the same genomic segment in which SP has a point mutation;
PM - ploidy of the subpopulation with the point mutation (SP);
PM_cnv - ploidy of genomic segment (overlapping the point mutation), in the subpopulation with CNV (SP_cnv).
colName
The subpopulation specific value assigned to each copy number fragment. Possible values: PM_cnv, PM, PM_B. Default: PM_cnv.
keepAmbigSeg
Whether or not to assign ploidy to a subpopulation, $SP_i$, for a segment containing multiple $SP_i$ specific ploidities, at least two of which have distinct magnitudes. If set to TRUE, the median ploidy is assigned as segment ploidy. Setting this parameter to TRUE is not recommended as the output will include segment-assignements where subpopulation specific ploidy is ambiguous. Repeating circular binary segmentation with less stringent parameters typically reduces segment length and thus the prevalence of ambiguous assignements. Default: FALSE.