# Infer Copy Number Variation from Single-Cell RNA-Seq Data

## Documentation for package ‘infercnv’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

infercnv-package | infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data
add_to_seurat | add_to_seurat()
apply_median_filtering | apply_median_filtering
color.palette | Helper function allowing greater control over the steps in a color palette.
CreateInfercnvObject | CreateInfercnvObject
filterHighPNormals | filterHighPNormals: Filter the HMM identified CNV's by the CNV's posterior probability of belonging to a normal state.
HMM_states | infercnv object result of the processing of run() in the HMM example, to be used for other examples.
infercnv | The infercnv Class
infercnv-class | The infercnv Class
inferCNVBayesNet | inferCNVBayesNet: Run Bayesian Network Mixture Model To Obtain Posterior Probabilities For HMM Predicted States
infercnv_annots_example | Generated classification for 10 normal cells and 10 tumor cells.
infercnv_data_example | 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.
infercnv_genes_example | Downsampled gene coordinates file from GrCh37
infercnv_object_example | infercnv object result of the processing of run() in the example, to be used for other examples.
MCMC_inferCNV | MCMC_inferCNV class
MCMC_inferCNV-class | MCMC_inferCNV class
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
plot_subclusters | Plot a heatmap of the data in the infercnv object with the subclusters being displayed as annotations.
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()
_PACKAGE | infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data