LoadFastaData: Load the SNP data from fasta files.
In atSNP: Affinity test for identifying regulatory SNPs

Description Usage Arguments Value Author(s) Examples

Load SNP data.

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

`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.

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.

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

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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")