Man pages for WhopGenome
High-Speed Processing of VCF, FASTA and Alignment Data

bgzf_compressCompress file with bgzip
fai_buildBuild a .fai-index for the given FASTA file.
fai_closeCloses a file previously opened with fai_open
fai_openOpen a faidx-indexed FASTA file
fai_query2Extract a part of a FASTA sequence.
fai_query4Extract a part of a FASTA sequence.
fai_reopenReopen a FAIhandle that has become stale.
tabix_buildBuild a tabix index file for fast access to...
tabix_closeClose Tabix-indexed file
tabix_getregionReturn the currently selected region of the given tabix file.
tabix_openOpen Tabix-indexed file for subsequent access with other...
tabix_readRead a line from a tabix_open()'ed file
tabix_reopenReopen a Tabix-indexed file if the filehandle became invalid.
tabix_restartregionReset the currently selected region to the beginning.
tabix_setregionReopen a Tabix-indexed file if the filehandle became invalid.
vcf_addfilterAdd a condition for SNP filtering from VCF files.
vcf_buildindexBuild Tabix-index required for processing VCF files.
vcf_clearfiltersRemoves all filter steps.
vcf_closeClose a VCF file previously opened with vcf_open.
vcf_countSNPsCount how many entries in the selected region
vcf_describefiltersPrints description of current filter rules
vcf_eorDetermine whether all lines in the selected region have been...
vcf_getChromReturn a specific piece of information from the last line...
vcf_getcontignamesReturn the contig/chromosome identifiers used in the VCF file
vcf_getfieldnamesReturn a vector with the field names used in the VCF file.
vcf_getheaderlineReturn one of the header lines of the VCF file
vcf_getnumcontigsGet the number of different contigs/chromosomes stored in the...
vcf_getregionGet description of currently selected chromosomal region.
vcf_isINDELDetermines whether the last vcf_parse-call returned a InDel...
vcf_isSNPDetermines whether the last vcf_parse-call returned a SNP...
vcf_openOpen the specified VCF file and return a filehandle for...
vcf_parseNextSNPRead until next SNP or next line and buffer it
vcf_readLineDFRead a line of data from the given VCF file and return it as...
vcf_readLineRawRead a line of data from the given VCF file and return it as...
vcf_readLineVecRead a line of data from the given VCF file and return the...
VCF_read_snp_diplo_bial_int_altpresence(OBSOLETE) Read batch of biallelic SNP data into matrices
vcf_reopenReopen a closed or stale VCF file handle.
vcf_restartregionLet subsequent read calls return from the start of the...
vcf_rule.disableDisable and enable processing of a rule
vcf_rule.setactionSets the kind of action to take when a rule matches (or does...
vcf_rule.setcolumnSet column a rule should examine.
vcf_rule.setcomparisonSet comparison operation for filtering rule.
vcf_rule.setfieldSet field or key of filtering rule.
vcf_rule.setrefvaluesSet reference values for a filtering rule's comparison...
vcf_selectsamplesSet or query the active sample selection for a given VCF file...
vcf_setregionSet region from which to return genome variation data.
VCF_snpmat_diplo_bial_geno_filteredRead SNP matrices in one of various representations.
vcf_validReturns whether a VCF file handle is valid and usable.
whop.eg.abbrevForOrganismLook up the organism prefix for the .org.eg.db databases from...
whop.eg.chromosomeReturn the chromosome on which the gene identified by the...
whop.eg.eg_lookupReturn all entries in an EG organism's data table for all...
whop.eg.eg_lookupAllReturn all entries in an EG organism's data table for a given...
whop.eg.eg_lookupSingleReturn the first entry in an EG organism's data table for a...
whop.eg.eg_RevLookupPerform a reverse lookup on one of the EG organism database's...
whop.eg.enzymeTurn an Enzyme identifier into a Entrez identifier.
whop.eg.fromAccnumTurn a GenBank accession number into a Entrez identifier.
whop.eg.fromAliasTurn an Alias into a Entrez identifier.
whop.eg.fromEnsemblTurn an Ensembl identifier into a Entrez identifier.
whop.eg.fromEnsemblProtTurn an Ensembl Protein identifier into a Entrez identifier.
whop.eg.fromEnsemblTransTurn an Ensemble transcript identifier into a Entrez...
whop.eg.fromEnzymeTurn an Enzyme nomenclature identifier into a Entrez...
whop.eg.fromGOTurn a GO term identifier into a related Entrez identifier.
whop.eg.fromGO2AllEgsReturn all Entrez identifiers related to a given GO term.
whop.eg.fromOmimTurn an OMIM identifier into a Entrez identifier.
whop.eg.fromPathTurn a KEGG pathway identifier into related Entrez...
whop.eg.fromPmidTurn an PMID identifier into a Entrez identifier.
whop.eg.fromRefseqTurn a Refseq identifier into a Entrez identifier.
whop.eg.fromUnigeneTurn an Unigene identifier into a Entrez identifier.
whop.eg.fromUniprotTurn an Uniprot identifier into a Entrez identifier.
whop.eg.genenameFind the gene name for a given Entrez identifier
whop.eg.goIdsReturns GO term identifiers related to the given Entrez...
whop.eg.installdbDownload and install the Bioconductor EG database for a given...
whop.eg.keggpathwaysLook up KEGG pathway identifiers related to the given Entrez...
whop.eg.load_orgdbLoad and, if necessary, install a Bioconductor EG database...
whop.eg.OrganismReturns the organism's name for which the current...
whop.eg.orgdb_loadedFind out whether a certain organism's Bioconductor EG...
whop.eg.regionLook up the start and end of the gene identified by the given...
whop.eg.selectOrganismSelect the organism to query with subsequent whop.eg calls...
whop.eg.toAccnumLook up for an Entrez identifier the corresponding GenBank...
whop.eg.toAliasLook up the corresponding common alias for an Entrez...
whop.eg.toEnsemblLook up for an Entrez identifier the corresponding Ensembl...
whop.eg.toEnsemblProtLook up for an Entrez identifier the corresponding Ensembl...
whop.eg.toEnsemblTransLook up for an Entrez identifier the corresponding Ensembl...
whop.eg.toEnzymeLook up for an Entrez identifier the corresponding Enzyme...
whop.eg.toGOLook up for an Entrez identifier the corresponding GO terms.
whop.eg.toOmimLook up the OMIM identifier(s) corresponding to an Entrez...
whop.eg.toPathLook up the Pathway identifier(s) corresponding to an Entrez...
whop.eg.toPmidLook up the Uniprot identifier(s) corresponding to an Entrez...
whop.eg.toRefseqLook up the Refseq identifier(s) corresponding to an Entrez...
whop.eg.toUnigeneLook up the Unigene identifier(s) corresponding to an Entrez...
whop.eg.toUniprotLook up the Uniprot identifier(s) corresponding to an Entrez...
whop.go.all_genes_for_termReturns all genes related to the given GO term
whop.go.connectEstablish a connection to the AmiGO database servers
whop.go.goid_likeReturn GO terms with identifiers typographically similar to...
whop.go.is_obsolete_byidCheck obsolescence of GO terms with similar accessions
whop.go.is_obsolete_bynameCheck obsolescence of GO terms with similar names
whop.go.loadLoad a GO term database from file
whop.go.matchReturn all GO terms matching the given one
whop.go.term_ancestorsReturns all ancestors of the given GO term.
whop.go.term_ancestors_similarReturn ancestral GO terms of similarly named GO term.
whop.go.term_childrenReturn child terms of the given term
whop.go.terms_matchReturns all terms with names similar to the given one.
whop.go.term_synonymsReturns GO terms synonymous with the given term
whop.kegg.pathway_urlProduces a URL to the KEGG website for a certain pathway
whop.ped.daughtersOfReturn all daughters of a given individual from a pedigree...
whop.ped.entriesOfReturn all entries from a pedigree dataset matching the list...
whop.ped.familyOfReturns all members of an individuals family
whop.ped.fathersReturn all fathers from a pedigree dataset
whop.ped.femalesReturn all females from a pedigree dataset
whop.ped.fromPopReturn all individuals belonging to a given population
whop.ped.loadLoad a pedigree dataset from a .PED file
whop.ped.malesReturn only the male individuals from a pedigree dataset
whop.ped.mothersGet all mothers stored in a pedigree file
whop.ped.namesGet all individual names
whop.ped.parentsOfReturn the parents of individuals
whop.ped.saveSave pedigree data to file
whop.ped.siblingsOfReturn list of siblings
whop.ped.sonsOfReturns all sons of the given individuals
WhopPkg-packageHigh-speed, high-specialisation population-scale whole-genome...
whop.ucsc.geneInfoReturn information from UCSC about a gene named precisely as...
whop.ucsc.geneInfoSimilarReturn information UCSC has about any genes with similar...
whop.ucsc.genesForRegionReturn a list of genes located in a certain region on a...
whop.ucsc.querySend a SQL query string to the UCSC Genome Browser SQL server
WhopGenome documentation built on May 1, 2019, 10:12 p.m.