subset.pyRAD.loci: Subsets a 'pyRAD.loci' object
In RADami: Phylogenetic Analysis of RADseq Data

Description Usage Arguments Details Value Author(s) See Also

This function returns a dataset (at this point, only in DNAStringSet format) from a pyRAD.loci object, subsetting by loci and taxa provided as arguments

## S3 method for class 'pyRAD.loci'
subset(x, loci = colnames(x$radSummary$inds.mat),
              taxa = row.names(x$radSummary$inds.mat),
		format = "DNAStringSet", reportInterval = 500, mins = 1,
		nucVarType = c("verystrict", "strict", "relaxed"),
		use.tidyName = FALSE,
		snpsOnly = FALSE, cores = 1, ...)

`x`	an object of class `pyRAD.loci`
`loci`	a character vector of loci to include; defaults to all loci
`taxa`	a character vector of taxa to include; defaults to all taxa
`format`	format for DNA matrix; at this point, only `DNAStringSet` is supported
`reportInterval`	interval (number of loci) for reporting progress
`mins`	minimum number of individuals required to return locus data
`nucVarType`	nucleotide variability to consider in screening for polymorphism: 'relaxed' for all nucleotides, including ambiguities other than 'N', and counting all variable sites; 'strict' for only A,C,G,T, still counting all variable sites; and 'verystrict' for only A,C,G,T, countin only parsimony- informative sites.
`use.tidyName`	choose whether names are passed through tidyName
`snpsOnly`	choose whether you only want to get SNPs back, or whole locus sequences
`cores`	how many processing cores to use; if `cores = 1`, `lapply` is used throughout instead of `mclapply`
`...`	additional arguments passed to tidyName

Probably it would make sense to wrap some of the functioning of gen.RAD.loci.datasets into this function, but for now they are separated.

A list with values:

`DNA`	a list of datasets, one per locus, defined by `format` argument
`variable`	a boolean vector, indicating which loci are variable according to the criterion provided in arguments
`ntaxa`	an integer vector, indicating how many taxa are in each locus