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

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Documentation for package ‘infercnv’ version 1.21.0

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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