ComputeMotifScore       Compute the scores for SNP effects on motifs.
ComputePValues          Compute p-values for affinity scores.
GetIUPACSequence        Get the IUPAC sequence of a motif.
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.
atSNP-package           atSNP: affinity tests for regulatory SNP
                        detection
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.
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.
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.
