groupOTU method

Share:

Description

group tree based on selected OTU, will traceback to MRCA

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
groupOTU(object, focus, group_name = "group", ...)

## S4 method for signature 'raxml'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'hyphy'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'apeBootstrap'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'beast'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'codeml'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'codeml_mlc'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'gg'
groupOTU(object, focus, group_name)

## S4 method for signature 'ggplot'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'jplace'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'nhx'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'phangorn'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'phylip'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'paml_rst'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'phylo'
groupOTU(object, focus, group_name = "group")

## S4 method for signature 'r8s'
groupOTU(object, focus, group_name = "group", tree = "TREE")

Arguments

object

supported objects, including phylo, paml_rst, codeml_mlc, codeml, jplace, beast, hyphy

focus

a vector of tip (label or number) or a list of tips.

group_name

name of the group, 'group' by default

...

additional parameter

tree

which tree selected

Value

group index

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.