atSNP-package: atSNP: affinity tests for regulatory SNP detection

In atSNP: Affinity test for identifying regulatory SNPs

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 [e-mail]

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

atSNP documentation built on April 28, 2020, 6:50 p.m.