ComputeMotifScore {atSNP} | R Documentation

## Compute the scores for SNP effects on motifs.

### Description

Compute the log-likelihood scores for motifs.

### Usage

    ComputeMotifScore(motif.lib, snp.info, ncores = 1)

### Arguments

`motif.lib` | A list object with the output format of function `LoadMotifLibrary`.
`snp.info` | A list object with the output format of function `LoadSNPData`.
`ncores` | An integer for the number of parallel process. Default: 1.

### Details

This function computes the binding affinity scores for both alleles at each SNP window. For each pair of SNP and motif, it finds the subsequence from both strand that maximizes the affinity binding score. It returns both the matching positions and the maximized affinity scores.

### Value

A list of two data.frame's. Field `snp.tbl` contains:

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.

Field `motif.score` contains:

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.

### Author(s)

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

### Examples

    data(example)
    ComputeMotifScore(motif_library, snpInfo, ncores = 2)

[Package atSNP version 1.2.0 Index]