LoadFastaData: Load the SNP data from fasta files.

In chandlerzuo/atSNP: Affinity test for identifying regulatory SNPs

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 [e-mail], Chandler Zuo [e-mail]

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")

chandlerzuo/atSNP documentation built on Oct. 31, 2020, 4:33 a.m.