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 |