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

## Documentation for package ‘infercnv’ version 1.4.0

- 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()
annots | Generated classification for 10 normal cells and 10 tumor cells.
apply_median_filtering | apply_median_filtering
color.palette | Helper function allowing greater control over the steps in a color palette.
CreateInfercnvObject | CreateInfercnvObject
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
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_obj | 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
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