Cancer Clone Finder

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Documentation for package ‘ccfindR’ version 1.7.0

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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