assignQuantityToMutation

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.

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

The name of the new column. Valid options are: <code>FPKM, CN_Estimate.</code>

quantityColumnLabel

Assigns a quantity to each mutated locus. Currently, the only assignable quantity is the average ploidy (among all cells) of the locus in which the mutation is embedded. Future releases will include the expression of the corresponding locus as estimated from RNA-Seq, as an additional assignable quantity.

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.

assignQuantityToMutation: Quantity Assignment (Ploidy)

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