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.

AuthorUlrich Wittelsbuerger [aut, cre], Heng Li [ctb], Bob Handsaker [ctb]
Date of publication2016-07-07 13:35:51
MaintainerUlrich Wittelsbuerger <ulrich.wittelsbuerger@uni-duesseldorf.de>
LicenseGPL (>= 2)
Version0.9.4

View on CRAN

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_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

Files in this package

WhopGenome
WhopGenome/inst
WhopGenome/inst/CITATION
WhopGenome/inst/COPYRIGHTS
WhopGenome/inst/extdata
WhopGenome/inst/extdata/ex.vcf.gz
WhopGenome/inst/extdata/ex.fasta.fai
WhopGenome/inst/extdata/ex.gff3
WhopGenome/inst/extdata/ex.vcf.gz.tbi
WhopGenome/inst/extdata/ex.gff3.gz.tbi
WhopGenome/inst/extdata/ex.vcf
WhopGenome/inst/extdata/ex.fasta
WhopGenome/inst/extdata/ex.gff3.gz
WhopGenome/src
WhopGenome/src/rdnapp_MEGA.h
WhopGenome/src/w_snpmat_str.cpp
WhopGenome/src/w_main.cpp
WhopGenome/src/Makevars
WhopGenome/src/t_Rifc.cpp
WhopGenome/src/w_snpmat_diplo.cpp
WhopGenome/src/t_main.cpp
WhopGenome/src/w_region.cpp
WhopGenome/src/tabix
WhopGenome/src/tabix/bam_endian.h
WhopGenome/src/tabix/kstring.c
WhopGenome/src/tabix/bgzf.c
WhopGenome/src/tabix/bgzf.h
WhopGenome/src/tabix/ksort.h
WhopGenome/src/tabix/knetfile.h
WhopGenome/src/tabix/index.c
WhopGenome/src/tabix/tabix.h
WhopGenome/src/tabix/bedidx.c
WhopGenome/src/tabix/kseq.h
WhopGenome/src/tabix/khash.h
WhopGenome/src/tabix/faidx.c
WhopGenome/src/tabix/razf.c
WhopGenome/src/tabix/knetfile.c
WhopGenome/src/tabix/razf.h
WhopGenome/src/tabix/kstring.h
WhopGenome/src/tabix/faidx.h
WhopGenome/src/w_tabix_internal.h
WhopGenome/src/w_dataframe.cpp
WhopGenome/src/t_region.cpp
WhopGenome/src/w_read.cpp
WhopGenome/src/t_read.cpp
WhopGenome/src/dummy.cc
WhopGenome/src/w_tools.cpp
WhopGenome/src/readdnapp.cpp
WhopGenome/src/w_snpmat_int.cpp
WhopGenome/src/functor_common.h
WhopGenome/src/t_info.cpp
WhopGenome/src/w_tools.h
WhopGenome/src/w_snpmat_fnc.cpp
WhopGenome/src/rdnapp_Fasta.h
WhopGenome/src/w_codemat.cpp
WhopGenome/src/w_vcf.h
WhopGenome/src/w_samples.cpp
WhopGenome/src/w_filtering.cpp
WhopGenome/src/w_common.h
WhopGenome/src/dynstorage.h
WhopGenome/src/w_tabix.h
WhopGenome/src/w_vcf.cpp
WhopGenome/src/rdnapp_Phylip.h
WhopGenome/src/Makevars.win
WhopGenome/src/faidx_ifc.cpp
WhopGenome/src/rdnapp_MAF.h
WhopGenome/src/w_rsupport.cpp
WhopGenome/src/w_rsupport.h
WhopGenome/NAMESPACE
WhopGenome/R
WhopGenome/R/x_eg_db.R WhopGenome/R/ZZZ_whopgenome.R WhopGenome/R/tabix.R WhopGenome/R/x_ucsc.R WhopGenome/R/x_go.R WhopGenome/R/filter.R WhopGenome/R/samples.R WhopGenome/R/file.R WhopGenome/R/bgzf.R WhopGenome/R/fai.R WhopGenome/R/read_simple.R WhopGenome/R/regions.R WhopGenome/R/misc.R WhopGenome/R/x_pedigree.R
WhopGenome/MD5
WhopGenome/DESCRIPTION
WhopGenome/man
WhopGenome/man/whop.eg.orgdb_loaded.Rd WhopGenome/man/vcf_readLineDF.Rd WhopGenome/man/whop.eg.eg_lookupAll.Rd WhopGenome/man/vcf_getfieldnames.Rd WhopGenome/man/vcf_getChrom.Rd WhopGenome/man/vcf_countSNPs.Rd WhopGenome/man/whop.eg.toUnigene.Rd WhopGenome/man/whop.eg.fromUniprot.Rd WhopGenome/man/whop.ped.familyOf.Rd WhopGenome/man/whop.ped.save.Rd WhopGenome/man/whop.eg.fromGO2AllEgs.Rd WhopGenome/man/fai_open.Rd WhopGenome/man/whop.ped.parentsOf.Rd WhopGenome/man/whop.ped.males.Rd WhopGenome/man/whop.eg.fromEnsembl.Rd WhopGenome/man/vcf_parseNextSNP.Rd WhopGenome/man/vcf_getnumcontigs.Rd WhopGenome/man/whop.eg.toRefseq.Rd WhopGenome/man/whop.eg.toOmim.Rd WhopGenome/man/whop.ped.entriesOf.Rd WhopGenome/man/fai_build.Rd WhopGenome/man/whop.go.term_ancestors.Rd WhopGenome/man/whop.go.connect.Rd WhopGenome/man/whop.eg.fromPmid.Rd WhopGenome/man/whop.eg.toEnsemblProt.Rd WhopGenome/man/vcf_setregion.Rd WhopGenome/man/whop.go.goid_like.Rd WhopGenome/man/vcf_readLineRaw.Rd WhopGenome/man/whop.ucsc.geneInfoSimilar.Rd WhopGenome/man/tabix_close.Rd WhopGenome/man/whop.eg.region.Rd WhopGenome/man/vcf_restartregion.Rd WhopGenome/man/whop.ped.fromPop.Rd WhopGenome/man/whop.kegg.pathway_url.Rd WhopGenome/man/vcf_describefilters.Rd WhopGenome/man/whop.eg.eg_RevLookup.Rd WhopGenome/man/whop.go.is_obsolete_byid.Rd WhopGenome/man/tabix_build.Rd WhopGenome/man/vcf_isSNP.Rd WhopGenome/man/whop.ped.names.Rd WhopGenome/man/VCF_snpmat_diplo_bial_geno_filtered.Rd WhopGenome/man/whop.eg.toEnsembl.Rd WhopGenome/man/vcf_selectsamples.Rd WhopGenome/man/whop.eg.fromUnigene.Rd WhopGenome/man/tabix_restartregion.Rd WhopGenome/man/whop.go.term_synonyms.Rd WhopGenome/man/vcf_valid.Rd WhopGenome/man/whop.eg.fromEnzyme.Rd WhopGenome/man/whop.eg.fromPath.Rd WhopGenome/man/whop.go.term_ancestors_similar.Rd WhopGenome/man/whop.eg.toAlias.Rd WhopGenome/man/VCF_read_snp_diplo_bial_int_altpresence.Rd WhopGenome/man/vcf_getheaderline.Rd WhopGenome/man/tabix_read.Rd WhopGenome/man/whop.eg.eg_lookup.Rd WhopGenome/man/whop.eg.selectOrganism.Rd WhopGenome/man/whop.ucsc.query.Rd WhopGenome/man/whop.eg.enzyme.Rd WhopGenome/man/whop.eg.toAccnum.Rd WhopGenome/man/whop.eg.installdb.Rd WhopGenome/man/whop.go.is_obsolete_byname.Rd WhopGenome/man/whop.eg.fromAccnum.Rd WhopGenome/man/whop.eg.toUniprot.Rd WhopGenome/man/whop.go.all_genes_for_term.Rd WhopGenome/man/vcf_rule.setcolumn.Rd WhopGenome/man/vcf_getcontignames.Rd WhopGenome/man/whop.eg.fromGO.Rd WhopGenome/man/vcf_close.Rd WhopGenome/man/whop.ped.sonsOf.Rd WhopGenome/man/vcf_clearfilters.Rd WhopGenome/man/whop.ped.fathers.Rd WhopGenome/man/whop.eg.genename.Rd WhopGenome/man/vcf_open.Rd WhopGenome/man/whop.go.match.Rd WhopGenome/man/fai_reopen.Rd WhopGenome/man/tabix_open.Rd WhopGenome/man/vcf_buildindex.Rd WhopGenome/man/whop.eg.toGO.Rd WhopGenome/man/whop.ped.siblingsOf.Rd WhopGenome/man/whop.eg.eg_lookupSingle.Rd WhopGenome/man/whop.eg.keggpathways.Rd WhopGenome/man/whop.ped.females.Rd WhopGenome/man/whop.eg.goIds.Rd WhopGenome/man/whop.eg.fromAlias.Rd WhopGenome/man/vcf_rule.setfield.Rd WhopGenome/man/vcf_rule.setaction.Rd WhopGenome/man/bgzf_compress.Rd WhopGenome/man/whop.go.load.Rd WhopGenome/man/whop.eg.fromEnsemblTrans.Rd WhopGenome/man/vcf_reopen.Rd WhopGenome/man/fai_close.Rd WhopGenome/man/whop.ped.mothers.Rd WhopGenome/man/whop.go.terms_match.Rd WhopGenome/man/fai_query4.Rd WhopGenome/man/whop.eg.abbrevForOrganism.Rd WhopGenome/man/whop.eg.Organism.Rd WhopGenome/man/vcf_getregion.Rd WhopGenome/man/whop.eg.fromEnsemblProt.Rd WhopGenome/man/vcf_rule.setrefvalues.Rd WhopGenome/man/whop.eg.chromosome.Rd WhopGenome/man/tabix_getregion.Rd WhopGenome/man/whop.ucsc.geneInfo.Rd WhopGenome/man/whop.eg.fromOmim.Rd WhopGenome/man/fai_query2.Rd WhopGenome/man/whop.eg.toEnzyme.Rd WhopGenome/man/vcf_readLineVec.Rd WhopGenome/man/vcf_rule.setcomparison.Rd WhopGenome/man/whop.eg.toPmid.Rd WhopGenome/man/whop.ped.load.Rd WhopGenome/man/whop.eg.fromRefseq.Rd WhopGenome/man/WhopPkg-package.Rd WhopGenome/man/whop.go.term_children.Rd WhopGenome/man/whop.eg.load_orgdb.Rd WhopGenome/man/tabix_reopen.Rd WhopGenome/man/vcf_rule.disable.Rd WhopGenome/man/whop.eg.toPath.Rd WhopGenome/man/vcf_isINDEL.Rd WhopGenome/man/tabix_setregion.Rd WhopGenome/man/whop.ucsc.genesForRegion.Rd WhopGenome/man/whop.eg.toEnsemblTrans.Rd WhopGenome/man/vcf_addfilter.Rd WhopGenome/man/whop.ped.daughtersOf.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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