summary.pyRAD.loci: Summary method for 'pyRAD.loci' objects

In andrew-hipp/RADami: Phylogenetic Analysis of RADseq Data

Summary method for pyRAD.loci objects

Description

This function provides the summary stats used by many functions in RADami

Usage

## S3 method for class 'pyRAD.loci'
summary(object, rm.na = TRUE, ...)

Arguments

object	an object of class pyRAD.loci
rm.na	Boolean: remove NA individuals from inds.mat, due to blank lines in pyRAD loci objects
...	not currently used, but maintained for consistency with default summary method

Details

This is currently called by default by read.pyRAD, creating a list object called radSummary in value for that object.

Value

A list with of the following objects:

num.loci	an integer, indicating how many loci there are in the object
tips.per.locus	a list of character vectors, enumerating the tips in each locus
break.vectors	a named character vector of the break lines between vectors, with names corresponding to locus names – completely redundant with the same object in the pyRAD.loci object
seqs.per.locus	a list of named character vectors, enumerating the sequences in each locus, named by tips
num.inds.per.locus	an integer vector, indicating how many individuals are in each locus
variable.loci	a boolean vector, indicating which loci are variable (only using the pyRAD break vectors)
inds.mat	a handy boolean matrix with individuals as the rows and loci as the columns; used in several places in RADami
locus.lengths	an integer vector, indicating the length of each locus

Note

Probably these functions could be teased apart to be more useful and save space, but for now they are left as is. At this point, there is actually a fair bit of redundancy.

Author(s)

Andrew Hipp

See Also

read.pyRAD, print.pyRAD.loci

andrew-hipp/RADami documentation built on Nov. 9, 2023, 5:40 p.m.