getPhyloTree {MesKit} | R Documentation |
getPhyloTree
getPhyloTree( maf, patient.id = NULL, method = "NJ", min.vaf = 0, min.ccf = 0, bootstrap.rep.num = 100, ... )
maf |
Maf or MafList object generated by |
patient.id |
Select the specific patients. Default NULL, all patients are included. |
method |
Approach to construct phylogenetic trees. Choose one of "NJ"(Neibor-Joining), "MP"(maximum parsimony), "ML"(maximum likelihood), "FASTME.ols" or "FASTME.bal". |
min.vaf |
The minimum value of vaf. Default 0. |
min.ccf |
The minimum value of CCF. Default 0 |
bootstrap.rep.num |
Bootstrap iterations. Default 100. |
... |
Other options passed to |
PhyloTree or phyloTreeList object
maf.File <- system.file("extdata/", "CRC_HZ.maf", package = "MesKit") clin.File <- system.file("extdata/", "CRC_HZ.clin.txt", package = "MesKit") ccf.File <- system.file("extdata/", "CRC_HZ.ccf.tsv", package = "MesKit") maf <- readMaf(mafFile=maf.File, clinicalFile = clin.File, ccfFile=ccf.File, refBuild="hg19") phyloTree <- getPhyloTree(maf)