Man pages for kmeRtone
Multi-Purpose and Flexible k-Meric Enrichment Analysis Software
| addAlphaCol | Add transparency to color. |
| bedToCoor | Convert a BED file to chromosome-separated csv files. |
| buildControl | Build control regions |
| buildKmerTable | Count k-mers from given sequence(s) and build a data.table of... |
| buildMidPatternKmerTable | Count k-mers with specified middle pattern from given... |
| buildRangedKmerTable | Count kmers from a sequence in given ranges and build a... |
| buildRESTurl | Function constructs a URL for a REST API call by appending... |
| calKmerSkew | Function calculates the skew of k-mers based on their... |
| calPWM | Calculate position weight matrix of overlapping sequences.... |
| catHeader | Function prints a given message in a formatted header with... |
| Coordinate | Loading, manipulating, and analyzing coordinate data. |
| countBaseComposition | Function performs an analysis of base composition including... |
| countChoppedKmers | Function chops k-mers within specified ranges of a sequence... |
| countDistribution | Function performs an analysis of the distribution of genomic... |
| countKmers | Count k-mers from string(s) using a simple hash table. |
| countMidPatternContext2 | Locate a middle sequence pattern and count its sequence... |
| countMidPatternKmers | Count Relevant K-mers with Specified Middle Pattern from... |
| countPointContext2 | Ccount sequence context of given point positions. |
| countRangedKmers | Count k-mers in given ranges of a sequence. |
| countRevCompKmers | Count reverse complement sequence from its opposite strand.... |
| countSlidingWindow | Count sequence content in a sliding window of a sequence. |
| countSlidingWindow2 | Count sequence content in a sliding window of a sequence. |
| count_substring_fixed | Count sequence content in a given sequence. |
| count_substring_regex | Count sequence content in a given sequence. |
| downloadNCBIGenomes | Function downloads genome fasta files from the NCBI FTP... |
| downloadUCSCgenome | Function downloads chromosome-separated fasta genome... |
| example_genome_coor | Example genome coordinate file |
| example_kmeRtone_score | Example 2-mer enrichment/depletion scores |
| EXPLORE | Function generates various exploratory analyses. |
| extractKmers | Extract k-mers from a given Coordinate object and Genome... |
| generateGenicElementCoor | Function processes UCSC genePred tables to generate... |
| generateIntergenicCoor | Resolve and generate genic element coordinates from UCSC... |
| getCOSMICauthURL | Get COSMIC authenticated URL. |
| getCOSMICcancerGeneCensus | Get Cancer Gene Census (CGC) from COSMIC database. |
| getCOSMIClatestVersion | Function retrieves the latest version information of the... |
| getCOSMICmutantExport | Function downloads the latest Cosmic Mutant Export data from... |
| getEnsemblData | A generic function to get Ensembl data persistently from a... |
| getEnsemblRegionFeatures | Get features of a given region. |
| getEnsemblVariantFeatures | Get features of given variant IDs. |
| getEnsemblVariantFeatures_serial | Get features of given variant IDs. |
| getGnomADvariants | Get gnomAD VCF file using tabix. |
| getICTVvirusMetadataResource | Get Virus Metadata Resource (VMR) from International... |
| getNCBIassemblySummary | Get NCBI assembly summary. |
| getScores | Function calculates scores for k-mers based on case and... |
| getUCSCgenePredTable | Retrieve Gene Prediction Table from UCSC for a Given Genome |
| getVCFmetainfo | Read VCF metainfo file using tabix. |
| initKmerTable | Initialise k-mer table with all possible k-mers |
| Kmer_Table | A R6 class wrapper for data.table |
| kmeRtone | kmeRtone all-in-one user interface |
| loadCoordinate | Build Coordinate object. |
| loadGenome | Build Genome object. |
| loadGenomicContents | Function calculates various genomic content metrics based on... |
| mapKmers | Map k-mers of a given sequence and coordinate |
| mergeCoordinate | Merge overlapping or continuous regions. |
| mixColors | Mix color |
| NCBI_Genome | Class constructor - build NCBI Genome object |
| partitionCoordinate | Partition overlapping or continuous regions. |
| persistentDownload | Download file until successful |
| readBED | Read a BED file. One-based indexing is enforced. |
| readFASTA | Read FASTA files. |
| readVCF | Read VCF file using tabix. |
| readVCF2 | Read VCF file using tabix. |
| removeRegion | Remove overlapping region in coordinate 'data.table'. |
| reverseComplement | Get reverse complement sequence of DNA |
| SCORE | Calculate susceptibility scores for k-mers in case and... |
| scoreKmers | Function calculates the Z-score for each k-mer based on the... |
| selectGenomesForCrossSpeciesStudy | Select genomes for cross-species studies. |
| selectRepresentativeFromASM | Select the best representative species from the NCBI assembly... |
| simulatePopulation | Simulate a population given ranges of chromosome sequence to... |
| splitFASTA | Split a FASTA file by header. |
| STUDY_ACROSS_POPULATIONS | Study k-mer composition of selected COSMIC causal cancer... |
| STUDY_ACROSS_SPECIES | Study k-mer composition across species. |
| STUDY_CANCER_GENES | Study k-mer composition of causal cancer genes from COSMIC... |
| STUDY_GENIC_ELEMENTS | Study k-mer composition across species. |
| system3 | A system2 wrapper. If anything happen, just give me error! |
| trimCoordinate | Trim out-of-bound coordinates |
| UCSC_Genome | Class constructor - build Genome object |
| writeBED | Write a BED file. Zero-based indexing is enforced. |
| writeFASTA | Write FASTA files. |
| writeVCF | Write VCF file and compress using bgzip. |
