CreateInfercnvObject    CreateInfercnvObject
HMM_states              infercnv object result of the processing of
                        run() in the HMM example, to be used for other
                        examples.
MCMC_inferCNV-class     MCMC_inferCNV class
add_to_seurat           add_to_seurat()
annots                  Generated classification for 10 normal cells
                        and 10 tumor cells.
apply_median_filtering
                        apply_median_filtering
data                    Generated SmartSeq2 expression data with 10
                        normal cells and 10 tumor cells. This is only
                        to demonstrate how to use methods, not actual
                        data to be used in an analysis.
filterHighPNormals      filterHighPNormals: Filter the HMM identified
                        CNV's by the CNV's posterior probability of
                        belonging to a normal state.
genes                   Downsampled gene coordinates file from GrCh37
inferCNVBayesNet        inferCNVBayesNet: Run Bayesian Network Mixture
                        Model To Obtain Posterior Probabilities For HMM
                        Predicted States
infercnv-class          The infercnv Class
infercnv-package        infercnv: Infer Copy Number Variation from
                        Single-Cell RNA-Seq Data
infercnv_obj            infercnv object result of the processing of
                        run() in the example, to be used for other
                        examples.
mcmc_obj                infercnv object result of the processing of
                        inferCNVBayesNet in the example, to be used for
                        other examples.
plot_cnv                Plot the matrix as a heatmap, with cells as
                        rows and genes as columns, ordered according to
                        chromosome
plot_per_group          plot_per_group
run                     run() : Invokes a routine inferCNV analysis to
                        Infer CNV changes given a matrix of RNASeq
                        counts.
sample_object           sample_object
validate_infercnv_obj   validate_infercnv_obj()
