Man pages for hongzhonglu/Yeastspot3D
Mutation mapping analysis with protein 3D structure for yeast
| annotateSNP | SNP annotation Annotate the SNP data based on the genome... |
| changeATCG | Nucleotide conversion for the gene from minus strand |
| checkTanslatedProtein | Protein sequence quality check |
| chooseStrain | Choose strains which belong to the same group |
| clumpsAnalysis | Mutation enrichment analysis |
| clusterAnalysis | Cluster summary |
| countMutationProtein | Count residues's mutation number |
| findPPosition | Obtain the mutation result of a nsSNP |
| getDomainCoordinate | Mapping domain coordinate onto the protein 3D structure |
| getGeneCoordinate | Parse the gene coordinate Obtain a list which contains the... |
| getGeneName | Get gene for each SNP |
| getGeneNameWithSNP | List genes with SNPs |
| getGeneNameWithSNP1 | List genes with SNPs |
| getHotPvalue | Get p-value for each cluster |
| getHotVertice | Get significant pairs |
| getMultipleMatchParameter | Get multiple mapping results for one element |
| getOriginalCoordinateProtein | Obtain protein residues coordinate |
| getProteinFromCDS | Translate CDS into Protein |
| getPvalue | Calculate p-value |
| getSampleWAP | Get the sampled WAP score |
| getSingleMatchParameter | Get single mapping result for one element |
| getTotalWAP | Get WAP |
| hotSpotAnalysis | Mutation hotspot analysis |
| loadPackageForSNPanalysis | Load essential packages |
| mappingCoordinateFrom3DtoProtein | Coordinate mapping between protein and the related structure |
| mergeActiveSiteInf | Merget protein active site together |
| mergeGeneAnnotationFeature | Merge genome annotation together |
| mergeHotspot | Merge hotspots |
| parseMutipleSite | Parse the complex site |
| parseSingleSite | Parse the simple site |
| pdbExFilter | Experimental PDB files filtration |
| pdbHomoFilter | Modeled PDB files filtration |
| pdb.ResidueDistance | Calculate the distance between each two alpha carbons |
| pdb.ResolutionAll | Obtain the resolution through parsing the pdb web |
| pdb.ResolutionEX | Obtain the resolution for one experimetal PDB file |
| pdb.Sequence | Get PDB residue sequence |
| plotNullDistribution | Plot the desity graph of WAP |
| PositionResidueSNP | Get residue mutation from nsSNP |
| preprocessSNP | Prepare SNPs list for one gene |
| printSNPforGene | Print the mutated residues |
| qualityCheckFromCDStoProtein | Check the gene annotation quality |
| removeStopCoden | Remove stop coden |
| ResidueSum | Summarize the mutated residues information |
| sampleStand | Standardize the mutation number |
| snpFilterBasedMAF | Filter snp value based on maf_value |
| splitAndCombine | Fast estabolish the mapping relation between two element |
