Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

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Documentation for package ‘kmeRtone’ version 1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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 k-mer counts.
buildMidPatternKmerTable	Count k-mers with specified middle pattern from given sequence(s) and build a data.table of k-mer counts.
buildRangedKmerTable	Count kmers from a sequence in given ranges and build a data.table of k-mer counts.
buildRESTurl	Function constructs a URL for a REST API call by appending query parameters.
calKmerSkew	Function calculates the skew of k-mers based on their occurrence in positive and negative strands.
calPWM	Calculate position weight matrix of overlapping sequences. Simulation of human population is based on single nucleotide variation.
catHeader	Function prints a given message in a formatted header with borders.
Coordinate	Loading, manipulating, and analyzing coordinate data.
countBaseComposition	Function performs an analysis of base composition including sequence frequency, PWM calculations, and G/C content at various window sizes.
countChoppedKmers	Function chops k-mers within specified ranges of a sequence and counts them. It uses either a substring method or functionalities from the Biostrings package.
countDistribution	Function performs an analysis of the distribution of genomic cases.
countKmers	Count k-mers from string(s) using a simple hash table.
countMidPatternContext2	Locate a middle sequence pattern and count its sequence context.
countMidPatternKmers	Count Relevant K-mers with Specified Middle Pattern from Sequence String(s)
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. Build for k-mer table generated from initKmerTable function but applicable to others with the same format.
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 database. Users can provide either organism names or an assembly summary data table.
downloadUCSCgenome	Function downloads chromosome-separated fasta genome sequences from the UCSC database. Users can specify a genome name, an output folder, and a specific chromosome or chromosomes. There's an option to choose the download method as well.
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 objects
generateGenicElementCoor	Function processes UCSC genePred tables to generate coordinates for various genic elements like introns, exons, CDS, UTRs, and upstream and downstream regions. It handles these coordinates with consideration for strand sensitivity and genome information.
generateIntergenicCoor	Resolve and generate genic element coordinates from UCSC genePred table.
getCOSMICauthURL	Get COSMIC authenticated URL.
getCOSMICcancerGeneCensus	Get Cancer Gene Census (CGC) from COSMIC database.
getCOSMIClatestVersion	Function retrieves the latest version information of the COSMIC database and the associated genome version by scraping data from the COSMIC website.
getCOSMICmutantExport	Function downloads the latest Cosmic Mutant Export data from the COSMIC database. It requires the user to be registered with COSMIC for non-commercial use. The function constructs the URL for the latest mutant export file, authenticates the URL, and then downloads the data.
getEnsemblData	A generic function to get Ensembl data persistently from a URL. This is an internal function used by other getEnsemblXXX functions.
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 Committee on Taxonomy of Viruses (ICTV)
getNCBIassemblySummary	Get NCBI assembly summary.
getScores	Function calculates scores for k-mers based on case and control k-mer counts.
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
kmeRtone	kmeRtone all-in-one user interface
Kmer_Table	A R6 class wrapper for data.table
loadCoordinate	Build Coordinate object.
loadGenome	Build Genome object.
loadGenomicContents	Function calculates various genomic content metrics based on the provided genome object.
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 control regions.
scoreKmers	Function calculates the Z-score for each k-mer based on the observed case counts and expected case counts under the null hypothesis.
selectGenomesForCrossSpeciesStudy	Select genomes for cross-species studies.
selectRepresentativeFromASM	Select the best representative species from the NCBI assembly summary.
simulatePopulation	Simulate a population given ranges of chromosome sequence to mutate.
splitFASTA	Split a FASTA file by header.
STUDY_ACROSS_POPULATIONS	Study k-mer composition of selected COSMIC causal cancer genes across human populations worldwide.
STUDY_ACROSS_SPECIES	Study k-mer composition across species.
STUDY_CANCER_GENES	Study k-mer composition of causal cancer genes from COSMIC Cancer Gene Census (CGC) database.
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.