Find ancestors within an oncogenetic tree.

Description

ancestors finds all the ancestors of the given vertex within the tree starting from itself up to the root. least.common.ancestor finds the common ancestor of two vertices that is closest to them (and farthest from the root).

Usage

   ancestors(otree, vertex)
   least.common.ancestor(otree, v1, v2)

Arguments

Value

For ancestors: a character vector giving the names of the ancestors of vertex. The first element is vertex, and the last one is “Root”.

For least.common.ancestor: a character value with the name of the least common ancestor of v1 and v2.

See Also

oncotree.fit

Examples

  data(ov.cgh)
  ov.tree <- oncotree.fit(ov.cgh)
  ancestors(ov.tree, "4q-")
  ancestors(ov.tree, "Xp-")
  least.common.ancestor(ov.tree, "4q-","Xp-")  #"5q-"

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Oncotree)
Loading required package: boot
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Oncotree/ancestors.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ancestors
> ### Title: Find ancestors within an oncogenetic tree.
> ### Aliases: ancestors least.common.ancestor
> ### Keywords: models
> 
> ### ** Examples
> 
>   data(ov.cgh)
>   ov.tree <- oncotree.fit(ov.cgh)
>   ancestors(ov.tree, "4q-")
[1] "4q-"  "5q-"  "Root"
>   ancestors(ov.tree, "Xp-")
[1] "Xp-"  "8p-"  "5q-"  "Root"
>   least.common.ancestor(ov.tree, "4q-","Xp-")  #"5q-"
[1] "5q-"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>