R: A Toy Dataset in Class seq.data

seq.data {phyclust} | R Documentation

## A Toy Dataset in Class seq.data

### Description

A toy dataset, `seq.data.toy`, with 100 nucleotide sequences and 200 sites in 4 clusters. `seq.data.gap` contains some missing values indicated by "-".

### Format

This data contains a list with a `seq.data` structure described in the ‘Details’ section.

### Details

A toy dataset is generated to demonstrate phyclust. It has 100 nucleotide sequences and 200 sites in 4 clusters where the ancestral tree height 0.15 and the descendant tree height 0.09, and sequences are evolved by a HKY85 model.

The structre of class `seq.data` is a list containing:

`code.type` | either "NUCLEOTIDE" or "SNP".
`info` | header for phylip file.
`nseq` | number of sequences, N.
`seqlen` | length of sequences, L.
`seqname` | sequence names.
`org.code` | original codes, dim = N*L.
`org` | transfered ids, dim = N*L.
`byrow` | TRUE for dim = N*L, FALSE for transpose.

### Author(s)

Wei-Chen Chen wccsnow@gmail.com

### References

Phylogenetic Clustering Website: https://snoweye.github.io/phyclust/

### See Also

`print.seq.data`.

### Examples

    ## Not run:
    library(phyclust, quiet = TRUE)

    seq.data.toy
    seq.data.gap

    par(mfrow = c(1, 2))
    plotdots(seq.data.toy$org)
    plotdots(seq.data.gap$org)

    ## End(Not run)

[Package phyclust version 0.1-30 Index]