| 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. |