MCMC_inferCNV-class: MCMC_inferCNV class

In broadinstitute/infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data

MCMC_inferCNV class

Description

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.

Slots

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

broadinstitute/infercnv documentation built on April 26, 2024, 4:11 a.m.