Usage
# S3 method for 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, ...)Arguments
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