MCMC_inferCNV-class: MCMC_inferCNV class
In infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data

Description Slots

Uses Markov Chain Monte Carlo (MCMC) and Gibbs sampling to estimate the posterior probability of being in one of six Copy Number Variation states (states: 0, 0.5, 1, 1.5, 2, 3) for CNV's identified by inferCNV's HMM. Posterior probabilities are found for the entire CNV cluster and each individual cell line in the CNV.

bugs_model: BUGS model.
sig: fitted values for cell lines, 1/standard deviation to be used for determining the distribution of each cell line
mu: Mean values to be used for determining the distribution of each cell line
group_id: ID's given to the cell clusters.
cell_gene: List containing the Cells and Genes that make up each CNV.
cnv_probabilities: Probabilities of each CNV belonging to a particular state from 0 (least likely)to 1 (most likely).
cell_probabilities: Probabilities of each cell being in a particular state, from 0 (least likely)to 1 (most likely).
args: Input arguments given by the user
cnv_regions: ID for each CNV found by the HMM
States: States that are identified and (depending on posterior MCMC input methods) modified.