seq.data: A Toy Dataset in Class seq.data

In snoweye/phyclust: Phylogenetic Clustering (Phyloclustering)

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\times L.
org	transfered ids, dim = N\times L.
byrow	TRUE for dim = N\times L, FALSE for transpose.

Author(s)

Wei-Chen Chen [e-mail]

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)

snoweye/phyclust documentation built on Sept. 12, 2023, 5 a.m.