addsamptree |
To determine whether the sampled tree will be accepted |
AML43 |
SNA input for primary tumor and relapse genome of leukemia patient from Ding et al. Nature 2012. |
canopy.BIC |
To get BIC as a model selection criterion |
canopy.cluster |
EM algorithm for multivariate clustering of SNAs |
canopy.cluster.Estep |
E-step of EM algorithm for multivariate clustering of SNAs |
canopy.cluster.Mstep |
M-step of EM algorithm for multivariate clustering of SNAs |
canopy.output |
To generate a posterior tree |
canopy.plottree |
To plot tree inferred by Canopy |
canopy.post |
Posterior evaluation of MCMC sampled trees |
canopy.sample |
MCMC sampling in tree space |
canopy.sample.cluster |
MCMC sampling in tree space with pre-clustering of SNAs |
canopy.sample.cluster.nocna |
MCMC sampling in tree space with pre-clustering of SNAs |
canopy.sample.nocna |
MCMC sampling in tree space |
getclonalcomposition |
To get clonal composition |
getCMCm |
To get major and minor copy per clone |
getCZ |
To get CNA genotyping matrix CZ |
getlikelihood |
To get likelihood of the tree |
getlikelihood.sna |
To get SNA likelihood of the tree |
getQ |
To get SNA-CNA genotyping matrix |
getVAF |
To get variant allele frequency (VAF) |
getZ |
To get SNA genotyping matrix Z |
initialcna |
To initialize positions of CNAs |
initialcnacopy |
To initialize major and minor copies of CNAs |
initialP |
To initialize clonal frequency matrix |
initialsna |
To initialize positions of SNAs |
MDA231 |
Dataset for project MDA231 |
MDA231_sampchain |
List of pre-sampled trees |
MDA231_tree |
Most likely tree from project MDA231 |
sampcna |
To sample CNA positions |
sampcnacopy |
To sample major and minor copies of CNAs |
sampP |
To sample clonal frequency |
sampsna |
To sample SNA positions |
sampsna.cluster |
To sample positions of SNA clusters |
sortcna |
To sort identified overlapping CNAs. |
toy |
Toy dataset for Canopy |
toy2 |
Toy dataset 2 for Canopy |
toy3 |
Toy dataset 3 for Canopy |