Copy number segments as obtained by circular binary segmentation. Data is derived from a Glioblastoma tumor (TCGA-06-0152-01).

datasets

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.

Noemi Andor

expands

Expanding Ploidy and Allele-Frequency on Nested Subpopulations

cbs function

Numeric matrix with 120 rows (one per copy-number segment) and 4 columns:
	 chr - the chromosome 
	 startpos - genomic position at which copy-number segment starts.
	 endpos - genomic position at which copy-number segment ends.
	 CN_Estimate - average copy-number of the segment among all cells.

cbs: Matrix of copy number fragments

Description

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