read.big.fasta: Reading big FASTA alignments

Description

This function splits huge FASTA alignments in chunks.

Usage

read.big.fasta(filename,populations=FALSE,outgroup=FALSE,window=2000,
               SNP.DATA=FALSE,include.unknown=FALSE,
               parallized=FALSE,FAST=TRUE,big.data=FALSE)

Arguments

filename

the basepath of the FASTA alignment

outgroup

vector of outgroup sequences

populations

list of populations

window

chunk size: number of columns

SNP.DATA

should be switched to TRUE if you use SNP data in alignment format

include.unknown

including unknown positions in the biallelic.matrix

parallized

only on UNIX ! Parallel computation

FAST

Fast computation. see readData()

big.data

using the ff-package

Value

The function creates an object of class "GENOME" --------------------------------------------------------- Following Slots will be filled in the "GENOME" object --------------------------------------------------------- rll{ Slot Description 1. n.sites total number of sites 2. n.biallelic.sites number of biallelic sites 3. region.names names of each reagion 4. region.data some detail data informations }

Details

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Examples

Run this code

# GENOME.class <- read.big.fasta("Alignment.fas")
# GENOME.class
# GENOME.class@region.names
# GENOME.class.slide <- sliding.window.transform(GENOME.class,100,100)
# GENOME.class <- neutrality.stats(GENOME.class,FAST=TRUE)
# show the result:
# get.sum.data(GENOME.class)
# GENOME.class@region.data

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