Clone Identification from Single Cell Data

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Documentation for package ‘cardelino’ version 1.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

assign_cells_to_clones	Assign cells to clones from cardelino results
assign_scores	Scoring the simulation in assignment of singlets and doublets
A_clone	A matrix of read numbers of alternative alleles for clone ID
A_germline	A matrix of read numbers of alternative alleles
binaryPRC	Precision-recall curve for binary label prediction
binaryROC	ROC curve for binary label prediction
Clone ID	Infer clonal identity of single cells
clone_id	Infer clonal identity of single cells
clone_id_EM	Infer clonal identity of single cells
clone_id_Gibbs	Infer clonal identity of single cells
colMatch	Column match between two matrices by minimum mean absolute difference
Config_all	A list of tree configuration
devianceIC	Deviance Information Criterion for cardelino model
donor_read_simulator	Reads simulator for donor identification
D_clone	A matrix of sequencing depths for clone ID
D_germline	A matrix of sequencing depths
D_input	A matrix of sequencing depths
get_logLik	Log likelihood of clone_id model It returns P(A, D | C, I, theta0, theta1)
get_snp_matrices	Get SNP data matrices from VCF object(s)
get_tree	Get a clonal tree from a configuration matrix
Geweke_Z	Geweke diagnostic for MCMC sampling.
heatmap.theme	The theme of heatmaps for prob_heatmap and sites_heatmap
heat_matrix	Plot heatmap from a matrix
load_cellSNP_vcf	Load sparse matrices A and D from cellSNP VCF file with filtering SNPs
load_GT_vcf	Load genotype VCF into numeric values: 0, 1, or 2
mixBinom	EM algorithm for estimating binomial mixture model
mtx_to_df	Convert a matrix to data frame
multiPRC	Precision-recall curve for multi-class prediction
plot_config_diffs	Define a publication-style plot theme
plot_tree	Plot a phylogenetic tree
predMixBinom	Predicted probability from learned binomial mixture model
prob_heatmap	Plot a heatmap for probability of clone assignment
pub.theme	Define a publication-style plot theme
read_vcf	Read a VCF file into R session
rowArgmax	Column index of the maximum value for each row in a matrix
rowMax	Maximum value for each row in a matrix
sample_seq_depth	Update matrix D with manually selected missing rate
sample_tree_SNV	Down sample number of SNVs in the tree
sim_read_count	Synthetic reads generator for genetic variants
tree	A tree object
tree_3clone	A tree object
tree_4clone	A tree object
tree_5clone	A tree object
vc_heatmap	Plot a variant-cell heatmap for cell clonal assignment