LoadFastaData {atSNP} | R Documentation |
Load SNP data.
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
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")