RADami (version 1.1-2)

read.pyRAD: Read in data from pyRAD

Description

This function begins essentially all analyses in this package. It reads in the pyRAD loci file and stores it in a form to facilitate a variety of downstream analyses coded in this package.

Usage

read.pyRAD(filename, reportInterval = 20000,
	         breakLinesSeparate = FALSE, 
           doSummary = TRUE, ...)

Arguments

filename

name of the pyRAD loci file

reportInterval

how often to report progress while reading and processing files

breakLinesSeparate

are there separate break lines (blank) and summary lines (not blank) between loci in the pyRAD file?

doSummary

should summary.pyRAD.loci be run on the object and appended to the end?

…

extra arguments to be passed along to readLines

Value

A list with the following items:

tips

a character vector of the tips for each sequence

seqs

a character vector of all sequences

breaks

an integer vector indexing the lines that are breaks between loci

break.vectors

a named character vector of the break lines between vectors, with names corresponding to locus names

cons

a named character vector of the lines summarizing each locus, with names corresponding to locus names; if breakLinesSeparate = F, this is identical to break.vectors

locus.index

an index corresponding to seqs and tips, indicating what locus each belongs to

file.read

name of the file read in

timestamp

timestamp for exiting the function

radSummary

an object of class summary.pyRAD.loci, if called, which it is by default

Details

As written, this function has a lot of summary embedded in it. The default doSummary = TRUE should be left for the other higher-level functions to work properly

See Also

summary.pyRAD.loci