Man pages for davismcc/cardelino
Clone and Donor 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
cardelino-packageClone and Donor Identification from Single Cell Data
clone_idInfer clonal identity of single cells
Config_allA list of tree configuration
D_cloneA matrix of sequencing depths for clone ID
D_germlineA matrix of sequncing depths
D_inputA matrix of sequncing depths
donor_idDonor deconvolution of scRNA-seq data
donor_id_EMEM algorithm for donor deconvolution with or without...
donor_id_GibbsGibbs sampler for donor deconvolution without genotypes.
get_doublet_GTGenerate genotype for doublets
get_prob_labelGet the clone label from the assignmnet probabilities.
get_prob_valueGet the collapsed probability value
get_snp_matricesGet SNP data matrices from VCF object(s)
Geweke_ZGeweke diagnostic for MCMC sampling.
heatmap.themeThe theme of heatmaps for prob_heatmap and sites_heatmap
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
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 Sept. 26, 2018, 4:55 a.m.