A numeric or integer matrix of bins x n.cells containing copy number quantals for each bin[i] and cell[j] where bins represent a common genomic segment across all cells (either a fixed with, variable binning, or .seg data). A quantal is the log ratio x the ploidy. This data can be constructed using a variable length bin and CBS (Varbin algorithm) (Baslan et al 2012.), and implemented on Ginkgo, or from hmmCopy. These are upstream analyses to the package.
The copy numbers in this alpha release is composed of uniform distributions from 0 to 100 or 120 across all bins
Alternatively, the cnq can be a binary (0,1) matrix representing presence or absence of specific mutations, or a ternary (0,1,2) representing genotypes as the number of alternate allele copies.
A matrix containg the bin x n.cell copy number estimations
bins, in rows from j..n
cellIDs, in columns from i..n
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