# Affinity test for identifying regulatory SNPs

## Documentation for package ‘atSNP’ version 1.29.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

atSNP-package | atSNP: affinity tests for regulatory SNP detection
ComputeMotifScore | Compute the scores for SNP effects on motifs.
ComputePValues | Compute p-values for affinity scores.
dtMotifMatch | Compute the augmented matching subsequence on SNP and reference allele s.
encode_motif | A motif library containing 2065 motifs downloaded from http://compbio.mit.edu/encode-motifs/motifs.txt.
encode_motifinfo | The information for the motif library downloaded from http://compbio.mit.edu/encode-motifs/motifs.txt.
GetIUPACSequence | Get the IUPAC sequence of a motif.
jaspar_motif | A motif library containing 593 motifs downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.
jaspar_motifinfo | The information for the motif library downloaded from http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/pfm_all .txt.
LoadFastaData | Load the SNP data from fasta files.
LoadMotifLibrary | Load position weight matrices.
LoadSNPData | Load the SNP information and code the genome sequences around the SNP locations.
MatchSubsequence | Compute the matching subsequence.
motif_library | A sample motif library.
motif_match | Composit logo plotting input containing motif scores, the matching subsequences and the augmented matching subsequences on SNP and reference allele
motif_scores | Scores for the sample snp data computed based on the motif data.
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.
prior | Default stationary distribution for nucleotide sequences in the reference genome.
snpInfo | A data set for SNP information.
snp_tbl | A data frame for SNP information.
transition | Default transition probability matrix for nucleotide sequences in the reference genome.