# Cancer Clone Finder

## Documentation for package ‘ccfindR’ version 1.8.0

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

## Help Pages

ccfindR-package | ccfindR: Cancer Clone FindeR
assignCelltype | Cell type assignment via GSEA
basis | Basis matrices in an Object
basis-method | Basis matrix accessor
basis<- | Generics for basis matrix assignment
basis<--method | Modify basis matrices
build_tree | Build tree connecting clusters at different ranks
ccfindR | ccfindR: Cancer Clone FindeR
cell_map | Plot heatmap of clustering coefficient matrix
cluster_id | Assign cells into clusters
coeff | Coefficient matrices in an Object
coeff-method | Coefficient matrix accessor
coeff<- | Generics for coefficient matrix assignment
coeff<--method | Modify coefficient matrices
colData-method | Sample annotation accessor
colData<--method | Cell annotation assignment
counts-method | Accessor for count matrix
counts<--method | Assignment of count matrix
dbasis | Basis SD matrix accessor
dbasis-method | Basis SD matrix accessor
dbasis<- | Basis SD matrix assignment
dbasis<--method | Modify dbasis matrices
dcoeff | Coeff SD matrix accessor
dcoeff-method | Coeffcient SD matrix accessor
dcoeff<- | Coeff SD matrix assignment
dcoeff<--method | Modify dcoeff matrices
factorize | Maximum likelihood factorization
feature_map | Plot heatmap of basis matrix
filter_cells | Filter cells with quality control criteria
filter_genes | Filter genes with quality control criteria
gene_map | Plot heatmap of metagene matrix
measure | Factorization measures in an Object
measure-method | Rank measure accessor
measure<- | Generics for factorization measure assignment
measure<--method | Modify factorization measure
meta_gene.cv | Meta gene table with CV
meta_genes | Find metagenes from basis matrix
newick | Generate Newick format tree string from tree list object
normalize_count | Normalize count data
optimal_rank | Determine optimal rank
plot-method | Class 'scNMFSet' for storing input data and results
plot_genes | Plot gene variance distributions
plot_tree | Plot cluster tree
ranks | Rank values in an Object
ranks-method | Rank accessor
ranks<- | Generics for ranks assignment
ranks<--method | Modify ranks
read_10x | Read 10x data and generate scNMF object
remove_zeros | Remove rows or columns that are empty from an object
rename_tips | Rename tips of trees with cell types
rowData-method | Feature annotation accessor
rowData<--method | Gene annotation assignment
scNMFSet | Create 'scNMFSet' object
scNMFSet-class | Class 'scNMFSet' for storing input data and results
show-method | Display object
simulate_data | Generate simulated data for factorization
simulate_whx | Simulate factor matrices and data using priors
vb_factorize | Bayesian NMF inference of count matrix
visualize_clusters | Visualize clusters
write_10x | Write 10x data files
write_meta | Write meta genes to a file
[-method | Subsetting scNMFSet object