getPhyloTree {MesKit} | R Documentation

## getPhyloTree

### Description

getPhyloTree

### Usage

    getPhyloTree(
      maf,
      patient.id = NULL,
      method = "NJ",
      min.vaf = 0,
      min.ccf = 0,
      bootstrap.rep.num = 100,
      ...
    )

### Arguments

`maf` | Maf or MafList object generated by `readMaf` function
`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 `subMaf`

### Value

PhyloTree or phyloTreeList object

### Examples

    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)

[Package MesKit version 1.4.0 Index]