genotypes.pyRAD.loci: Generates genotypes from a 'subset.pyRAD.loci' object

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

Generates genotypes from a subset.pyRAD.loci object

Description

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

Usage

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)

Arguments

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

Details

current not tightly integrated with hierfstat, but designed to be used by it

Value

data.frame of genotypes

Author(s)

Andrew Hipp

See Also

subset.pyRAD.loci

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