LoadFastaData: Load the SNP data from fasta files.

In kinsigne/atSNP_modified: Affinity test for identifying regulatory SNPs.

Description

Load SNP data.

Usage

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

Arguments

ref.data	Fastq file name for the reference allele sequences.
snp.data	Fastq file name for the SNP allele sequences.
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)

Chandler Zuo [e-mail]

Examples

## Not run: LoadFastaData("http://pages.stat.wisc.edu/~keles/atSNP-Data/sample_1.fasta", "http://pages.stat.wisc.edu/~keles/atSNP-Data/sample_2.fasta")

kinsigne/atSNP_modified documentation built on May 23, 2019, 4:24 p.m.