VCF_read_snp_diplo_bial_int_altpresence
                        (OBSOLETE) Read batch of biallelic SNP data
                        into matrices
VCF_snpmat_diplo_bial_geno_filtered
                        Read SNP matrices in one of various
                        representations.
WhopGenome-package      High-speed, high-specialisation
                        population-scale whole-genome variation and
                        sequence data access
bgzf_compress           Compress file with bgzip
fai_build               Build a .fai-index for the given FASTA file.
fai_close               Closes a file previously opened with fai_open
fai_open                Open a faidx-indexed FASTA file
fai_query2              Extract a part of a FASTA sequence.
fai_query4              Extract a part of a FASTA sequence.
fai_reopen              Reopen a FAIhandle that has become stale.
tabix_build             Build a tabix index file for fast access to
                        tab-separated-value formatted files.
tabix_close             Close Tabix-indexed file
tabix_getregion         Return the currently selected region of the
                        given tabix file.
tabix_open              Open Tabix-indexed file for subsequent access
                        with other tabix_ methods
tabix_read              Read a line from a tabix_open()'ed file
tabix_reopen            Reopen a Tabix-indexed file if the filehandle
                        became invalid.
tabix_restartregion     Reset the currently selected region to the
                        beginning.
tabix_setregion         Reopen a Tabix-indexed file if the filehandle
                        became invalid.
vcf_addfilter           Add a condition for SNP filtering from VCF
                        files.
vcf_buildindex          Build Tabix-index required for processing VCF
                        files.
vcf_clearfilters        Removes all filter steps.
vcf_close               Close a VCF file previously opened with
                        vcf_open.
vcf_countSNPs           Count how many entries in the selected region
vcf_describefilters     Prints description of current filter rules
vcf_eor                 Determine whether all lines in the selected
                        region have been read.
vcf_getChrom            Return a specific piece of information from the
                        last line processed with vcf_parseNextSNP or
                        vcf_parsenextline.
vcf_getcontignames      Return the contig/chromosome identifiers used
                        in the VCF file
vcf_getfieldnames       Return a vector with the field names used in
                        the VCF file.
vcf_getheaderline       Return one of the header lines of the VCF file
vcf_getnumcontigs       Get the number of different contigs/chromosomes
                        stored in the file
vcf_getregion           Get description of currently selected
                        chromosomal region.
vcf_isINDEL             Determines whether the last vcf_parse-call
                        returned a InDel (instead of SNP)
vcf_isSNP               Determines whether the last vcf_parse-call
                        returned a SNP (instead of InDel)
vcf_open                Open the specified VCF file and return a
                        filehandle for subsequent access.
vcf_parseNextSNP        Read until next SNP or next line and buffer it
vcf_readLineDF          Read a line of data from the given VCF file and
                        return it as a data frame
vcf_readLineRaw         Read a line of data from the given VCF file and
                        return it as a string without postprocessing.
vcf_readLineVec         Read a line of data from the given VCF file and
                        return the fields as vector elements
vcf_reopen              Reopen a closed or stale VCF file handle.
vcf_restartregion       Let subsequent read calls return from the start
                        of the currently set region.
vcf_rule.disable        Disable and enable processing of a rule
vcf_rule.setaction      Sets the kind of action to take when a rule
                        matches (or does not match).
vcf_rule.setcolumn      Set column a rule should examine.
vcf_rule.setcomparison
                        Set comparison operation for filtering rule.
vcf_rule.setfield       Set field or key of filtering rule.
vcf_rule.setrefvalues   Set reference values for a filtering rule's
                        comparison operation.
vcf_selectsamples       Set or query the active sample selection for a
                        given VCF file or get the entire list of
                        individuals.
vcf_setregion           Set region from which to return genome
                        variation data.
vcf_valid               Returns whether a VCF file handle is valid and
                        usable.
whop.eg.Organism        Returns the organism's name for which the
                        current database-set contains information.
whop.eg.abbrevForOrganism
                        Look up the organism prefix for the .org.eg.db
                        databases from Bioconductor
whop.eg.chromosome      Return the chromosome on which the gene
                        identified by the given Entrez ID lies.
whop.eg.eg_RevLookup    Perform a reverse lookup on one of the EG
                        organism database's sub-tables.
whop.eg.eg_lookup       Return all entries in an EG organism's data
                        table for all given identifiers
whop.eg.eg_lookupAll    Return all entries in an EG organism's data
                        table for a given identifier
whop.eg.eg_lookupSingle
                        Return the first entry in an EG organism's data
                        table for a given identifier
whop.eg.enzyme          Turn an Enzyme identifier into a Entrez
                        identifier.
whop.eg.fromAccnum      Turn a GenBank accession number into a Entrez
                        identifier.
whop.eg.fromAlias       Turn an Alias into a Entrez identifier.
whop.eg.fromEnsembl     Turn an Ensembl identifier into a Entrez
                        identifier.
whop.eg.fromEnsemblProt
                        Turn an Ensembl Protein identifier into a
                        Entrez identifier.
whop.eg.fromEnsemblTrans
                        Turn an Ensemble transcript identifier into a
                        Entrez identifier.
whop.eg.fromEnzyme      Turn an Enzyme nomenclature identifier into a
                        Entrez identifier.
whop.eg.fromGO          Turn a GO term identifier into a related Entrez
                        identifier.
whop.eg.fromGO2AllEgs   Return all Entrez identifiers related to a
                        given GO term.
whop.eg.fromOmim        Turn an OMIM identifier into a Entrez
                        identifier.
whop.eg.fromPath        Turn a KEGG pathway identifier into related
                        Entrez identifiers.
whop.eg.fromPmid        Turn an PMID identifier into a Entrez
                        identifier.
whop.eg.fromRefseq      Turn a Refseq identifier into a Entrez
                        identifier.
whop.eg.fromUnigene     Turn an Unigene identifier into a Entrez
                        identifier.
whop.eg.fromUniprot     Turn an Uniprot identifier into a Entrez
                        identifier.
whop.eg.genename        Find the gene name for a given Entrez
                        identifier
whop.eg.goIds           Returns GO term identifiers related to the
                        given Entrez identifier.
whop.eg.installdb       Download and install the Bioconductor EG
                        database for a given organism
whop.eg.keggpathways    Look up KEGG pathway identifiers related to the
                        given Entrez identifier.
whop.eg.load_orgdb      Load and, if necessary, install a Bioconductor
                        EG database for a given organism.
whop.eg.orgdb_loaded    Find out whether a certain organism's
                        Bioconductor EG database has been loaded
whop.eg.region          Look up the start and end of the gene
                        identified by the given Entrez ID.
whop.eg.selectOrganism
                        Select the organism to query with subsequent
                        whop.eg calls and load the appropiate
                        database(s).
whop.eg.toAccnum        Look up for an Entrez identifier the
                        corresponding GenBank Accession number.
whop.eg.toAlias         Look up the corresponding common alias for an
                        Entrez identifier.
whop.eg.toEnsembl       Look up for an Entrez identifier the
                        corresponding Ensembl identifiers.
whop.eg.toEnsemblProt   Look up for an Entrez identifier the
                        corresponding Ensembl Protein identifiers.
whop.eg.toEnsemblTrans
                        Look up for an Entrez identifier the
                        corresponding Ensembl transcript identifiers.
whop.eg.toEnzyme        Look up for an Entrez identifier the
                        corresponding Enzyme identifiers.
whop.eg.toGO            Look up for an Entrez identifier the
                        corresponding GO terms.
whop.eg.toOmim          Look up the OMIM identifier(s) corresponding to
                        an Entrez identifier
whop.eg.toPath          Look up the Pathway identifier(s) corresponding
                        to an Entrez identifier
whop.eg.toPmid          Look up the Uniprot identifier(s) corresponding
                        to an Entrez identifier
whop.eg.toRefseq        Look up the Refseq identifier(s) corresponding
                        to an Entrez identifier
whop.eg.toUnigene       Look up the Unigene identifier(s) corresponding
                        to an Entrez identifier
whop.eg.toUniprot       Look up the Uniprot identifier(s) corresponding
                        to an Entrez identifier
whop.go.all_genes_for_term
                        Returns all genes related to the given GO term
whop.go.connect         Establish a connection to the AmiGO database
                        servers
whop.go.goid_like       Return GO terms with identifiers
                        typographically similar to the given one
whop.go.is_obsolete_byid
                        Check obsolescence of GO terms with similar
                        accessions
whop.go.is_obsolete_byname
                        Check obsolescence of GO terms with similar
                        names
whop.go.load            Load a GO term database from file
whop.go.match           Return all GO terms matching the given one
whop.go.term_ancestors
                        Returns all ancestors of the given GO term.
whop.go.term_ancestors_similar
                        Return ancestral GO terms of similarly named GO
                        term.
whop.go.term_children   Return child terms of the given term
whop.go.term_synonyms   Returns GO terms synonymous with the given term
whop.go.terms_match     Returns all terms with names similar to the
                        given one.
whop.kegg.pathway_url   Produces a URL to the KEGG website for a
                        certain pathway
whop.ped.daughtersOf    Return all daughters of a given individual from
                        a pedigree dataset
whop.ped.entriesOf      Return all entries from a pedigree dataset
                        matching the list of given identifiers.
whop.ped.familyOf       Returns all members of an individuals family
whop.ped.fathers        Return all fathers from a pedigree dataset
whop.ped.females        Return all females from a pedigree dataset
whop.ped.fromPop        Return all individuals belonging to a given
                        population
whop.ped.load           Load a pedigree dataset from a .PED file
whop.ped.males          Return only the male individuals from a
                        pedigree dataset
whop.ped.mothers        Get all mothers stored in a pedigree file
whop.ped.names          Get all individual names
whop.ped.parentsOf      Return the parents of individuals
whop.ped.save           Save pedigree data to file
whop.ped.siblingsOf     Return list of siblings
whop.ped.sonsOf         Returns all sons of the given individuals
whop.ucsc.geneInfo      Return information from UCSC about a gene named
                        precisely as specified
whop.ucsc.geneInfoSimilar
                        Return information UCSC has about any genes
                        with similar names
whop.ucsc.genesForRegion
                        Return a list of genes located in a certain
                        region on a certain chromosome
whop.ucsc.query         Send a SQL query string to the UCSC Genome
                        Browser SQL server
