atSNP-package {atSNP} | R Documentation

## atSNP: affinity tests for regulatory SNP detection

### Description

atSNP implements the affinity test for large sets of SNP-motif interactions using the importance sampling algorithm. Users may identify SNPs that potentially may affect binding affinity of transcription factors. Given a set of SNPs and a library of motif position weight matrices (PWMs), atSNP provides two main functions for analyzing SNP effects: (i) the binding affinity score for each allele and each PWM and the p-values for allele-specific binding affinity scores (ii) the p-values for affinity score changes between the two alleles for each SNP. Compared to other bioinformatics tools that provide similar functionalities, atSNP is highly scalable.

The atSNP main functions are:

1. `LoadMotifLibrary` - Load position weight matrices

2. `LoadSNPData` - Load the SNP information and code the genome sequences around the SNP locations

3. `LoadFastaData` - Load the SNP data from fasta files

4. `ComputeMotifScore` - Compute the scores for SNP effects on motifs

5. `ComputePValues` - Compute p-values for affinity scores

Some helper functions are:

1. `MatchSubsequence` - Compute the matching subsequence

2. `GetIUPACSequence` - Get the IUPAC sequence of a motif

3. `dtMotifMatch` - Compute the augmented matching subsequence on SNP and reference alleles

The composite logo plotting function is:

1. `plotMotifMatch` - Plot sequence logos of the position weight matrix of the motif and sequences of its corresponding best matching augmented subsequence on the reference and SNP allele

### Author(s)

Chandler Zuo Sunyoung Shin sunyoung.shin@utdallas.edu

### References

Zuo, Chandler, Shin, Sunyoung, and Keles, Sunduz. (2015). atSNP: Transcription factor binding affinity testing for regulatory SNP detection. Bioinformatics 31 (20): 3353-5.

### See Also

atSNP vignette for more information

[Package atSNP version 1.0.0 Index]