genotypes.pyRAD.loci: Generates genotypes from a 'subset.pyRAD.loci' object
In RADami: Phylogenetic Analysis of RADseq Data

Description Usage Arguments Details Value Author(s) See Also

Makes a dataframe of SNP calls from a pyRAD.loci object for export to hierfstat

genotypes.pyRAD.loci(dat, groups, loci = 'all', taxa = 'all',
	        useSnps = c('first', 'all'), concat = c(FALSE, TRUE),
					use.tidyName = FALSE,
					na.rm = c('none', 'columns', 'rows'),
					maxAlleles = 2,
					tidyVals = c('-', '.','>', '_', ' '),
					sortByGroups = TRUE,
					variable.only = FALSE, make.dummy.column = TRUE,
					alleleDigits = 1,
					toInteger = TRUE, missingData = "00",
					cores = 1)

`dat`	an object of class `subset.pyRAD.loci`
`groups`	a list of vectors, each vector designating a set of individuals to count for each group
`loci`	a character vector of loci to include; defaults to all loci
`taxa`	a character vector of taxa to include; defaults to all taxa
`useSnps`	whether to use the first SNP in each locus or all
`concat`	boolean: whether to concatenate SNPs or return by locus
`use.tidyName`	choose whether or not to use `tidyName` when matching names
`na.rm`	whether to remove missin data by columns, by rows, or not at all
`maxAlleles`	maximum number of alleles per locus
`tidyVals`	characters to be stripped out by tidyName, if using
`sortByGroups`	boolean: whether to sort snps by groups
`variable.only`	boolean: whether to keep only variable sites
`make.dummy.column`	boolean: whether to add a dummy column when there is only one SNP (currently added as a work-around for `wc`)
`alleleDigits`	how many digits per allele
`toInteger`	boolean: whether to return SNPs as integers
`missingData`	string to use for missing data
`cores`	how many processing cores to use; if `cores = 1`, `lapply` is used throughout instead of `mclapply`