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. |