Man pages for davismcc/cardelino
Clone Identification from Single Cell Data

A_cloneA matrix of read numbers of alternative alleles for clone ID
A_germlineA matrix of read numbers of alternative alleles
assign_cells_to_clonesAssign cells to clones from cardelino results
assign_scoresScoring the simulation in assignment of singlets and doublets
binaryPRCPrecision-recall curve for binary label prediction
binaryROCROC curve for binary label prediction
cardelino-packageClone Identification from Single Cell Data
clone_idInfer clonal identity of single cells
colMatchColumn match between two matrices by the minimum mean...
Config_allA list of tree configuration
D_cloneA matrix of sequencing depths for clone ID
devianceICDeviance Information Criterion for cardelino model
D_germlineA matrix of sequncing depths
D_inputA matrix of sequncing depths
donor_read_simulatorReads simulator for donor identification
get_logLikLog likelihood of clone_id model It returns P(A, D | C, I,...
get_snp_matricesGet SNP data matrices from VCF object(s)
get_treeGet a clonal tree from a configuration matrix
Geweke_ZGeweke diagnostic for MCMC sampling.
heatmap.themeThe theme of heatmaps for prob_heatmap and sites_heatmap
heat_matrixPlot heatmap from a matrix
load_cellSNP_vcfLoad sparse matrices A and D from cellSNP VCF file with...
load_GT_vcfLoad genotype VCF into numeric values: 0, 1, or 2
mtx_to_dfConvert a matrix to data frame
multiPRCPrecision-recall curve for multi-class prediction
plot_config_diffsDefine a publication-style plot theme
plot_treePlot a phylogenetic tree
prob_heatmapPlot a heatmap for probability of clone assignment
pub.themeDefine a publication-style plot theme
read_vcfRead a VCF file into R session
rowArgmaxColumn index of the maximum value for each row in a matrix
rowMaxMaximum value for each row in a matrix
sample_seq_depthUpdate matrix D with manully selected missing rate
sample_tree_SNVDown sample number of SNVs in the tree
sim_read_countSythetic reads generator for genetic variants
treeA tree object
tree_3cloneA tree object
tree_4cloneA tree object
tree_5cloneA tree object
vc_heatmapPlot a variant-cell heatmap for cell clonal assignment
davismcc/cardelino documentation built on Aug. 21, 2019, 3:31 p.m.