cnr: cnr: copy number, rounded

cnrR Documentation

cnr: copy number, rounded


The cnr object is a list of four relational matrices. The bins, genes, annotation, qc, chromInfo, and gene.index. The structure is inspired by Scanpy's AnnData to which cleverly integrates complex data into a simple architecture.




An object class list containg a rounded CNR

  • X, An integer matrix of bins x n.cells containing copy number estimations 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). 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.

    For mutations in single-cells, the cnq can be a binary incidence (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

    Unlike a standard rounding, we noticed that estimates for deletions and losses don't follow standard numeric rounding. We set a the thresholds of < 0.2 (average quantal estimate of the Y chromosome in females) for deletions (i.e. 0 copies); between 0.2 and 1.2 for losses (i.e. 1 copy); between 1.2 and 2.5 for 2 copies, and everything else standard numeric rounding.

  • genes, gene copy number interpolation from bins. The genes matrix is an interpolated, transposed, expansion of bins. The expansion is constructed internally using the expand2genes function.

  • Y, phenotypic data of single-cells, contains cells as rows, and phentypes in columns. Phenotypes can be information about individual samples, or if same-cell methods were used, the RNA expression from the same cell. #'

  • qc, quality control metrics. This matrix contains additional metadata that is technical, e.g. number of reads, MAPD estimates, and the PASS/FAIL qc.status for individual cells. contains cells as rows and metadata as columns

  • chromInfo, ordered chromosome information for the bins

  • gene.index, table to map bins to genes



SingerLab/gac documentation built on March 16, 2023, 2:52 p.m.