MatchSubsequence {atSNP} | R Documentation

## Compute the matching subsequence.

### Description

This function combines the SNP set, the motif library and the affinity score table and produce the matching subsequence found at each SNP location for each motif.

### Usage

    MatchSubsequence(snp.tbl, motif.scores, motif.lib, snpids = NULL,
      motifs = NULL, ncores = 1)

### Arguments

`snp.tbl` | A data.frame with the following information:
snpid | SNP id.
ref_seq | Reference allele nucleotide sequence.
snp_seq | SNP allele nucleotide sequence.
ref_seq_rev | Reference allele nucleotide sequence on the reverse strand.
snp_seq_rev | SNP allele nucleotide sequence on the reverse strand.
`motif.scores` | A data.frame with the following information:
motif | Name of the motif.
motif_len | Length of the motif.
ref_start, ref_end, ref_strand | Location of the best matching subsequence on the reference allele.
snp_start, snp_end, snp_strand | Location of the best matching subsequence on the SNP allele.
log_lik_ref | Log-likelihood score for the reference allele.
log_lik_snp | Log-likelihood score for the SNP allele.
log_lik_ratio | The log-likelihood ratio.
log_enhance_odds | Difference in log-likelihood ratio between SNP allele and reference allele based on the best matching subsequence on the reference allele.
log_reduce_odds | Difference in log-likelihood ratio between reference allele and SNP allele based on the best matching subsequence on the SNP allele.
`motif.lib` | A list of the position weight matrices for the motifs.
`snpids` | A subset of snpids to compute the subsequences. Default: NULL, when all snps are computed.
`motifs` | A subset of motifs to compute the subsequences. Default: NULL, when all motifs are computed.
`ncores` | The number of cores used for parallel computing.

### Value

A data.frame containing all columns in both `snp.tbl` and `motif.scores`. In addition, the following columns are added:

ref_match_seq | Best matching subsequence on the reference allele.
snp_match_seq | Best matching subsequence on the SNP allele.
ref_seq_snp_match | Subsequence on the reference allele corresponding to the best matching location on the SNP allele.
snp_seq_ref_match | Subsequence on the SNP allele corresponding to the best matching location on the reference allele.

### Author(s)

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

### Examples

    data(example)
    MatchSubsequence(motif_scores$snp.tbl, motif_scores$motif.scores,
    motif_library, ncores=2)

[Package atSNP version 1.2.0 Index]