read.pyRAD: Read in data from pyRAD

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

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

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

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

Author(s)

Andrew Hipp

See Also

summary.pyRAD.loci

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