Man pages for davismcc/cardelino
Clonal Analysis of Cells Using Single Cell Data

AA matrix of read numbers of alternative alleles
A_germlineA matrix of read numbers of alternative alleles
assign_curveCalculate assignability and accuracy along prob_gap
assign_macro_ROCCalculate macro ROC
assign_scoreAssess performance with simulated data
cardelino-packageClonal Analysis of Cells Using Single Cell Data
cell_assign_EMEM algorithm for assigning cells to clones and estimating...
cell_assign_GibbsGibbs sampling the cell assignments to cloens and the...
Config_allA list of tree configuration
confusion_heatmapPlot confusion heatmap for assessing simulation accuracy
DA matrix of sequncing depths
D_germlineA matrix of sequncing depths
D_inputA matrix of sequncing depths
donor_idGibbs sampler of the cell donor id and genotypes
get_Gibbs_probGet the probability matrix from Gibbs sampling on assignment
get_prob_gapGet the probability gap between the highest and the second...
get_prob_labelGet the clone label from the assignmnet probabilities.
get_prob_valueGet the collapsed probability value
get_snv_thetaCalculate the SNV specific allelic frequency (True postive...
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
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
sites_heatmapPlot a heatmap for number of mutation sites in each cell
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 July 4, 2018, 4:12 a.m.