assignQuantityToSP

Matrix in which each row corrsponds to a mutation. Has to contain at least the following columnnames: chr - the chrmosome on which each mutation is located;startpos - the genomic position of each mutation;SP - the SP to which the m

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 numbe

Assigns quantities to predicted SPs. Currently, the only assignable quantity are SP specific ploidies for the input genome segments (obtained by CBS).

Expanding Ploidy and Allele Frequency on Nested Subpopulations (ExPANdS) characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers.  The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results. Updates include (1)Phylogeny reconstruction based on SP specific copy number profiles. (2) Additional optional parameter "maxN" provided for function runExPANdS, specifying the maximal number of SNVs to be used for the clustering step. Restriction imposed by "maxN" is now used only for SP detection, not also for mutation assignment to SPs. (3) Relevant for whole genome sequencing (WGS) data: additional optional parameter "region" provided for function runExPANdS, specifying the region within which SNVs are to be used during clustering.

assignQuantityToSP: Quantity assignment (ploidy) to subpopulations

Description

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