LoadFastaData {atSNP} | R Documentation

## Load the SNP data from fasta files.

### Description

Load SNP data.

### Usage

    LoadFastaData(ref.filename = NULL, snp.filename = NULL,
      ref.urlname = NULL, snp.urlname = NULL, snpids = NULL,
      default.par = FALSE)

### Arguments

`ref.filename` | a fastq file name for the reference allele sequences.
`snp.filename` | a fastq file name for the SNP allele sequences.
`ref.urlname` | URL of a fastq file for the reference allele sequences.
`snp.urlname` | URL of a fastq file for the SNP allele sequences.
`snpids` | SNP IDs
`default.par` | A boolean for whether using the default Markov parameters. Default: FALSE.

### Value

A list object containing the following components:

sequence_matrix | A list of integer vectors representing the deroxyribose sequence around each SNP.
a1 | An integer vector for the deroxyribose at the SNP location on the reference genome.
a2 | An integer vector for the deroxyribose at the SNP location on the SNP genome.

The results are coded as: "A"-1, "C"-2, "G"-3, "T"-4.

### Author(s)

Sunyoung Shin sunyoung.shin@utdallas.edu, Chandler Zuo chandler.c.zuo@gmail.com

### Examples

    LoadFastaData(
    ref.urlname="http://pages.stat.wisc.edu/~keles/atSNP-Data/sample_1.fasta",
    snp.urlname="http://pages.stat.wisc.edu/~keles/atSNP-Data/sample_2.fasta")

[Package atSNP version 1.8.0 Index]