Man pages for chandlerzuo/atSNP
Affinity test for identifying regulatory SNPs
| atSNP-package | atSNP: affinity tests for regulatory SNP detection |
| comp_indel_mat_d | Compute the D matrix for indel calculation. |
| 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... |
| encode_motif | A motif library containing 2065 motifs downloaded from... |
| encode_motifinfo | The information for the motif library downloaded from... |
| GetIUPACSequence | Get the IUPAC sequence of a motif. |
| jaspar_motif | A motif library containing 593 motifs downloaded from... |
| jaspar_motifinfo | The information for the motif library downloaded from... |
| LoadFastaData | Load the SNP data from fasta files. |
| LoadMotifLibrary | Load position weight matrices. |
| LoadSNPData | Load the SNP information and code the genome sequences around... |
| MatchSubsequence | Compute the matching subsequence. |
| motif_library | A sample motif library. |
| motif_match | Composit logo plotting input containing motif scores, the... |
| motif_scores | Scores for the sample snp data computed based on the motif... |
| plotMotifMatch | Plot sequence logos of the position weight matrix of the... |
| prior | Default stationary distribution for nucleotide sequences in... |
| p_values_for_motif | Compute p-values for a single motif. |
| pval_with_less_var | Select p-value estimates with less variance. |
| snpInfo | A data set for SNP information. |
| snp_tbl | A data frame for SNP information. |
| transition | Default transition probability matrix for nucleotide... |
