summary.tree: Get a summary of a Newick-formatted tree, edge lengths, node...

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Get a summary of a Newick-formatted tree, edge lengths, node names, etc

Usage

## S3 method for class 'tree'
summary(object, ...)

Arguments

object	A character string containing a newick tree
...	Not currently used (exists for S3 compatibility)

Value

A data frame with a row for every node, containing columns: branch length (tparent), distance to root (troot), name, label (if tree labels present), and parent, rchild, lchild.

Author(s)

Melissa J. Hubisz and Adam Siepel

Examples

tree <- "(((hg18:0.01, panTro2:0.01)hg18-panTro2:0.07,
              (mm9:0.083220,rn4:0.090564)mm9-rn4:
             0.269385)hg18-rn4:0.020666,canFam2:0.193569);"
summary.tree(tree)
summary.tree(label.subtree(tree, "mm9-rn4", "rodent", include.leading=TRUE))

Example output

          name  tparent    troot parent lchild rchild
1         <NA>       NA 0.000000     NA      2      9
2     hg18-rn4 0.020666 0.020666      1      3      6
3 hg18-panTro2 0.070000 0.090666      2      4      5
4         hg18 0.010000 0.100666      3     NA     NA
5      panTro2 0.010000 0.100666      3     NA     NA
6      mm9-rn4 0.269385 0.290051      2      7      8
7          mm9 0.083220 0.373271      6     NA     NA
8          rn4 0.090564 0.380615      6     NA     NA
9      canFam2 0.193569 0.193569      1     NA     NA
          name  tparent    troot parent lchild rchild  label
1         <NA>       NA 0.000000     NA      2      9   <NA>
2     hg18-rn4 0.020666 0.020666      1      3      6   <NA>
3 hg18-panTro2 0.070000 0.090666      2      4      5   <NA>
4         hg18 0.010000 0.100666      3     NA     NA   <NA>
5      panTro2 0.010000 0.100666      3     NA     NA   <NA>
6      mm9-rn4 0.269385 0.290051      2      7      8 rodent
7          mm9 0.083220 0.373271      6     NA     NA rodent
8          rn4 0.090564 0.380615      6     NA     NA rodent
9      canFam2 0.193569 0.193569      1     NA     NA   <NA>

rphast documentation built on May 1, 2019, 9:26 p.m.