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
assign_scoresScoring the simulation in assignment of singlets and doublets
binaryPRCPrecision-recall curve for binary label prediction
cardelino-packageClone and Donor 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
D_germlineA matrix of sequncing depths
D_inputA matrix of sequncing depths
donor_idDonor deconvolution of scRNA-seq data, replaced by function...
donor_read_simulatorReads simulator for donor identification
get_doublet_GTGenerate genotype probability for doublets
get_doublet_thetaGenerate theta parameters for doublet genotype
get_ID_probInternal function to update cell assignement probability
get_snp_matricesGet SNP data matrices from VCF object(s)
Geweke_ZGeweke diagnostic for MCMC sampling.
GT_to_probConvert genotype matrix to genotype probability matrix
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
nega_beta_entropyNegative entropy value for beta distribution
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
transpose_GT_probTranspose genotype probability matrix
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
vireoDonor deconvolution of scRNA-seq data
vireo_coreVariational inference with a single run
vireo_flockVariational inference for donor deconvolution with or without...
davismcc/cardelino documentation built on Jan. 22, 2019, 2:20 p.m.