PopGenome (version 1.2.6)

region.as.fasta-methods: Extract a region as a FASTA file

Description

This generic function writes a FASTA file of the observed biallelic positions to the current workspace.

Usage

## S3 method for class 'GENOME':
region.as.fasta(object,region.id=FALSE,filename=FALSE,type=1,ref.chr=FALSE)

Arguments

object

an object of class "GENOME"

region.id

region of the genome

filename

name of the FASTA file

type

1: extract SNPs 2: extract all nucleotides

ref.chr

reference sequence

Examples

#GENOME.class       <- readSNP("Arabidopsis",CHR=1)
#GENOME.class.split <- splitting.data(GENOME.class, positions=list(100:200))
#region.as.fasta(GENOME.class.split,1,"my_fasta_file.fas")