WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Provides very fast access to whole genome, population scale variation data from VCF files and sequence data from FASTA-formatted files. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.

Install the latest version of this package by entering the following in R:
AuthorUlrich Wittelsbuerger [aut, cre], Heng Li [ctb], Bob Handsaker [ctb]
Date of publication2017-03-13 17:10:56
MaintainerUlrich Wittelsbuerger <ulrich.wittelsbuerger@uni-duesseldorf.de>
LicenseGPL (>= 2)

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Man pages

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...

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_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...

vcf_getChrom: Return a specific piece of information from the last line...

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...

vcf_getregion: Get description of currently selected chromosomal region.

vcf_isINDEL: Determines whether the last vcf_parse-call returned a InDel...

vcf_isSNP: Determines whether the last vcf_parse-call returned a SNP...

vcf_open: Open the specified VCF file and return a filehandle for...

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...

vcf_readLineRaw: Read a line of data from the given VCF file and return it as...

vcf_readLineVec: Read 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_reopen: Reopen a closed or stale VCF file handle.

vcf_restartregion: Let subsequent read calls return from the start of the...

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...

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...

vcf_selectsamples: Set or query the active sample selection for a given VCF file...

vcf_setregion: Set region from which to return genome variation data.

VCF_snpmat_diplo_bial_geno_filtered: Read SNP matrices in one of various representations.

vcf_valid: Returns whether a VCF file handle is valid and usable.

whop.eg.abbrevForOrganism: Look up the organism prefix for the .org.eg.db databases from...

whop.eg.chromosome: Return the chromosome on which the gene identified by the...

whop.eg.eg_lookup: Return all entries in an EG organism's data table for all...

whop.eg.eg_lookupAll: Return all entries in an EG organism's data table for a given...

whop.eg.eg_lookupSingle: Return the first entry in an EG organism's data table for a...

whop.eg.eg_RevLookup: Perform a reverse lookup on one of the EG organism database's...

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...

whop.eg.fromEnzyme: Turn an Enzyme nomenclature identifier into a Entrez...

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...

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...

whop.eg.installdb: Download and install the Bioconductor EG database for a given...

whop.eg.keggpathways: Look up KEGG pathway identifiers related to the given Entrez...

whop.eg.load_orgdb: Load and, if necessary, install a Bioconductor EG database...

whop.eg.Organism: Returns the organism's name for which the current...

whop.eg.orgdb_loaded: Find out whether a certain organism's Bioconductor EG...

whop.eg.region: Look up the start and end of the gene identified by the given...

whop.eg.selectOrganism: Select the organism to query with subsequent whop.eg calls...

whop.eg.toAccnum: Look up for an Entrez identifier the corresponding GenBank...

whop.eg.toAlias: Look up the corresponding common alias for an Entrez...

whop.eg.toEnsembl: Look up for an Entrez identifier the corresponding Ensembl...

whop.eg.toEnsemblProt: Look up for an Entrez identifier the corresponding Ensembl...

whop.eg.toEnsemblTrans: Look up for an Entrez identifier the corresponding Ensembl...

whop.eg.toEnzyme: Look up for an Entrez identifier the corresponding Enzyme...

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...

whop.eg.toPath: Look up the Pathway identifier(s) corresponding to an Entrez...

whop.eg.toPmid: Look up the Uniprot identifier(s) corresponding to an Entrez...

whop.eg.toRefseq: Look up the Refseq identifier(s) corresponding to an Entrez...

whop.eg.toUnigene: Look up the Unigene identifier(s) corresponding to an Entrez...

whop.eg.toUniprot: Look up the Uniprot identifier(s) corresponding to an Entrez...

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...

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.terms_match: Returns all terms with names similar to the given one.

whop.go.term_synonyms: Returns GO terms synonymous with the given term

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...

whop.ped.entriesOf: Return all entries from a pedigree dataset matching the list...

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

WhopPkg-package: High-speed, high-specialisation population-scale whole-genome...

whop.ucsc.geneInfo: Return information from UCSC about a gene named precisely as...

whop.ucsc.geneInfoSimilar: Return information UCSC has about any genes with similar...

whop.ucsc.genesForRegion: Return a list of genes located in a certain region on a...

whop.ucsc.query: Send a SQL query string to the UCSC Genome Browser SQL server


bgzf_compress Man page
fai_build Man page
fai_close Man page
fai_open Man page
fai_query2 Man page
fai_query3 Man page
fai_query4 Man page
fai_query5 Man page
fai_reopen Man page
read_snp_diplo_bial_int_altpresence Man page
read_snp_diplo_bial_int_nuclcodes Man page
read_snp_diplo_bial_str_01 Man page
read_snp_diplo_bial_str_allelechars Man page
read_snp_diplo_bial_str_nuclcodes Man page
tabix_build Man page
tabix_close Man page
tabix_getregion Man page
tabix_open Man page
tabix_read Man page
tabix_readraw Man page
tabix_reopen Man page
tabix_restartregion Man page
tabix_setregion Man page
vcf_addfilter Man page
vcf_buildindex Man page
vcf_clearfilters Man page
vcf_close Man page
vcf_countBiallelicSNPs Man page
vcf_countSNPs Man page
vcf_describefilters Man page
vcf_eor Man page
vcf_getAlt Man page
vcf_getChrom Man page
vcf_getcontignames Man page
vcf_getfieldnames Man page
vcf_getFilter Man page
vcf_getFormat Man page
vcf_getheaderline Man page
vcf_getID Man page
vcf_getInfo Man page
vcf_getInfoField Man page
vcf_getnumcontigs Man page
vcf_getPos Man page
vcf_getQual Man page
vcf_getRef Man page
vcf_getregion Man page
vcf_getSample Man page
vcf_getsamples Man page
vcf_getselectedsamples Man page
vcf_isINDEL Man page
vcf_isSNP Man page
vcf_open Man page
vcf_parseNextLine Man page
vcf_parseNextSNP Man page
VCF_readIntoCodeMatrix Man page
vcf_readLineDF Man page
vcf_readLineRaw Man page
vcf_readLineRawFiltered Man page
vcf_readLineVec Man page
vcf_readLineVecFiltered Man page
VCF_read_snp_diplo_bial_int_altpresence Man page
VCF_read_snp_diplo_bial_int_nuclcodes Man page
VCF_read_snp_diplo_bial_str_01 Man page
VCF_read_snp_diplo_bial_str_allelechars Man page
VCF_read_snp_diplo_bial_str_nuclcodes Man page
vcf_reopen Man page
vcf_restartregion Man page
vcf_rule.disable Man page
vcf_rule.enable Man page
vcf_rule.setaction Man page
vcf_rule.setcolumn Man page
vcf_rule.setcomparison Man page
vcf_rule.setfield Man page
vcf_rule.setrefvalues Man page
vcf_selectsamples Man page
vcf_setregion Man page
VCF_snpmat_anyplo_anyal_nucodes_filtered Man page
VCF_snpmat_anyplo_anyal_nucodes_unfiltered Man page
VCF_snpmat_anyplo_bial_nucodes_filtered Man page
VCF_snpmat_anyplo_bial_nucodes_unfiltered Man page
VCF_snpmat_diplo_anyal_geno_filtered Man page
VCF_snpmat_diplo_anyal_geno_unfiltered Man page
VCF_snpmat_diplo_anyal_hasalt_filtered Man page
VCF_snpmat_diplo_anyal_hasalt_unfiltered Man page
VCF_snpmat_diplo_anyal_ishet_filtered Man page
VCF_snpmat_diplo_anyal_ishet_unfiltered Man page
VCF_snpmat_diplo_anyal_nucodes_filtered Man page
VCF_snpmat_diplo_anyal_nucodes_unfiltered Man page
VCF_snpmat_diplo_bial_geno_filtered Man page
VCF_snpmat_diplo_bial_geno_unfiltered Man page
VCF_snpmat_diplo_bial_hasalt_filtered Man page
VCF_snpmat_diplo_bial_hasalt_unfiltered Man page
VCF_snpmat_diplo_bial_ishet_filtered Man page
VCF_snpmat_diplo_bial_ishet_unfiltered Man page
VCF_snpmat_diplo_bial_nucodes_filtered Man page
VCF_snpmat_diplo_bial_nucodes_unfiltered Man page
vcf_valid Man page
whop.eg.abbrevForOrganism Man page
whop.eg.chromosome Man page
whop.eg.eg_lookup Man page
whop.eg.eg_lookupAll Man page
whop.eg.eg_lookupSingle Man page
whop.eg.eg_RevLookup Man page
whop.eg.enzyme Man page
whop.eg.fromAccnum Man page
whop.eg.fromAlias Man page
whop.eg.fromEnsembl Man page
whop.eg.fromEnsemblProt Man page
whop.eg.fromEnsemblTrans Man page
whop.eg.fromEnzyme Man page
whop.eg.fromGO Man page
whop.eg.fromGO2AllEgs Man page
whop.eg.fromOmim Man page
whop.eg.fromPath Man page
whop.eg.fromPmid Man page
whop.eg.fromRefseq Man page
whop.eg.fromUnigene Man page
whop.eg.fromUniprot Man page
whop.eg.genename Man page
whop.eg.goIds Man page
whop.eg.installdb Man page
whop.eg.keggpathways Man page
whop.eg.load_orgdb Man page
whop.eg.Organism Man page
whop.eg.orgdb_loaded Man page
whop.eg.region Man page
whop.eg.selectOrganism Man page
whop.eg.toAccnum Man page
whop.eg.toAlias Man page
whop.eg.toEnsembl Man page
whop.eg.toEnsemblProt Man page
whop.eg.toEnsemblTrans Man page
whop.eg.toEnzyme Man page
whop.eg.toGO Man page
whop.eg.toOmim Man page
whop.eg.toPath Man page
whop.eg.toPmid Man page
whop.eg.toRefseq Man page
whop.eg.toUnigene Man page
whop.eg.toUniprot Man page
WhopGenome Man page
WhopGenome-package Man page
whop.go.all_genes_for_term Man page
whop.go.connect Man page
whop.go.goid_like Man page
whop.go.is_obsolete_byid Man page
whop.go.is_obsolete_byname Man page
whop.go.load Man page
whop.go.match Man page
whop.go.term_ancestors Man page
whop.go.term_ancestors_similar Man page
whop.go.term_children Man page
whop.go.terms_match Man page
whop.go.term_synonyms Man page
whop.kegg.pathway_url Man page
whop.ped.daughtersOf Man page
whop.ped.entriesOf Man page
whop.ped.familyOf Man page
whop.ped.fathers Man page
whop.ped.females Man page
whop.ped.fromPop Man page
whop.ped.load Man page
whop.ped.males Man page
whop.ped.mothers Man page
whop.ped.names Man page
whop.ped.parentsOf Man page
whop.ped.save Man page
whop.ped.siblingsOf Man page
whop.ped.sonsOf Man page
whop.ucsc.geneInfo Man page
whop.ucsc.geneInfoSimilar Man page
whop.ucsc.genesForRegion Man page
whop.ucsc.query Man page


R/x_eg_db.R R/ZZZ_whopgenome.R R/tabix.R R/x_ucsc.R R/x_go.R R/filter.R R/samples.R R/file.R R/bgzf.R R/fai.R R/read_simple.R R/regions.R R/misc.R R/x_pedigree.R
man/whop.eg.orgdb_loaded.Rd man/vcf_readLineDF.Rd man/whop.eg.eg_lookupAll.Rd man/vcf_eor.Rd man/vcf_getfieldnames.Rd man/vcf_getChrom.Rd man/vcf_countSNPs.Rd man/whop.eg.toUnigene.Rd man/whop.eg.fromUniprot.Rd man/whop.ped.familyOf.Rd man/whop.ped.save.Rd man/whop.eg.fromGO2AllEgs.Rd man/fai_open.Rd man/whop.ped.parentsOf.Rd man/whop.ped.males.Rd man/whop.eg.fromEnsembl.Rd man/vcf_parseNextSNP.Rd man/vcf_getnumcontigs.Rd man/whop.eg.toRefseq.Rd man/whop.eg.toOmim.Rd man/whop.ped.entriesOf.Rd man/fai_build.Rd man/whop.go.term_ancestors.Rd man/whop.go.connect.Rd man/whop.eg.fromPmid.Rd man/whop.eg.toEnsemblProt.Rd man/vcf_setregion.Rd man/whop.go.goid_like.Rd man/vcf_readLineRaw.Rd man/whop.ucsc.geneInfoSimilar.Rd man/tabix_close.Rd man/whop.eg.region.Rd man/vcf_restartregion.Rd man/whop.ped.fromPop.Rd man/whop.kegg.pathway_url.Rd man/vcf_describefilters.Rd man/whop.eg.eg_RevLookup.Rd man/whop.go.is_obsolete_byid.Rd man/tabix_build.Rd man/vcf_isSNP.Rd man/whop.ped.names.Rd man/VCF_snpmat_diplo_bial_geno_filtered.Rd man/whop.eg.toEnsembl.Rd man/vcf_selectsamples.Rd man/whop.eg.fromUnigene.Rd man/tabix_restartregion.Rd man/whop.go.term_synonyms.Rd man/vcf_valid.Rd man/whop.eg.fromEnzyme.Rd man/whop.eg.fromPath.Rd man/whop.go.term_ancestors_similar.Rd man/whop.eg.toAlias.Rd man/VCF_read_snp_diplo_bial_int_altpresence.Rd man/vcf_getheaderline.Rd man/tabix_read.Rd man/whop.eg.eg_lookup.Rd man/whop.eg.selectOrganism.Rd man/whop.ucsc.query.Rd man/whop.eg.enzyme.Rd man/whop.eg.toAccnum.Rd man/whop.eg.installdb.Rd man/whop.go.is_obsolete_byname.Rd man/whop.eg.fromAccnum.Rd man/whop.eg.toUniprot.Rd man/whop.go.all_genes_for_term.Rd man/vcf_rule.setcolumn.Rd man/vcf_getcontignames.Rd man/whop.eg.fromGO.Rd man/vcf_close.Rd man/whop.ped.sonsOf.Rd man/vcf_clearfilters.Rd man/whop.ped.fathers.Rd man/whop.eg.genename.Rd man/vcf_open.Rd man/whop.go.match.Rd man/fai_reopen.Rd man/tabix_open.Rd man/vcf_buildindex.Rd man/whop.eg.toGO.Rd man/whop.ped.siblingsOf.Rd man/whop.eg.eg_lookupSingle.Rd man/whop.eg.keggpathways.Rd man/whop.ped.females.Rd man/whop.eg.goIds.Rd man/whop.eg.fromAlias.Rd man/vcf_rule.setfield.Rd man/vcf_rule.setaction.Rd man/bgzf_compress.Rd man/whop.go.load.Rd man/whop.eg.fromEnsemblTrans.Rd man/vcf_reopen.Rd man/fai_close.Rd man/whop.ped.mothers.Rd man/whop.go.terms_match.Rd man/fai_query4.Rd man/whop.eg.abbrevForOrganism.Rd man/whop.eg.Organism.Rd man/vcf_getregion.Rd man/whop.eg.fromEnsemblProt.Rd man/vcf_rule.setrefvalues.Rd man/whop.eg.chromosome.Rd man/tabix_getregion.Rd man/whop.ucsc.geneInfo.Rd man/whop.eg.fromOmim.Rd man/fai_query2.Rd man/whop.eg.toEnzyme.Rd man/vcf_readLineVec.Rd man/vcf_rule.setcomparison.Rd man/whop.eg.toPmid.Rd man/whop.ped.load.Rd man/whop.eg.fromRefseq.Rd man/WhopPkg-package.Rd man/whop.go.term_children.Rd man/whop.eg.load_orgdb.Rd man/tabix_reopen.Rd man/vcf_rule.disable.Rd man/whop.eg.toPath.Rd man/vcf_isINDEL.Rd man/tabix_setregion.Rd man/whop.ucsc.genesForRegion.Rd man/whop.eg.toEnsemblTrans.Rd man/vcf_addfilter.Rd man/whop.ped.daughtersOf.Rd

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