assignQuantityToMutation

Matrix in which each row corresponds to a mutation. Has to contain at least the following column names: 
	chr - the chromosome on which each mutation is located;
	startpos - the genomic position of each mutation.

Matrix in which each row corresponds to a copy number segment as calculated by a circular binary segmentation algorithm. Has to contain at least the following column names:
	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.

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

quantityColumnLabel

verbose

Assigns a quantity to each mutated locus. Currently, the only assignable quantity is the average copy number (among all cells) of the locus in which the mutation is embedded.

Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data (<https://pubmed.ncbi.nlm.nih.gov/24177718/>). The model detects coexisting genotypes by leveraging run-specific tradeoffs between depth of coverage and breadth of coverage. This package predicts the number of clonal expansions, the size of the resulting subpopulations in the tumor bulk, the mutations specific to each subpopulation, tumor purity and phylogeny. The main function runExPANdS() provides the complete functionality needed to predict coexisting subpopulations from single nucleotide variations (SNVs) and associated copy numbers. The robustness of subpopulation predictions increases with the number of mutations provided. It is recommended that at least 200 mutations are used as input to obtain stable results. Updates in version 2.1 include: (i) new parameter ploidy in runExPANdS.R allows specification of non-diploid background ploidies (e.g. for near-triploid cell lines); (ii) parallel computing option is available.

assignQuantityToMutation: Quantity assignment (copy number) to mutations

Description

Usage

Arguments

Value

Examples