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.

Author
Ulrich Wittelsbuerger [aut, cre], Heng Li [ctb], Bob Handsaker [ctb]
Date of publication
2016-07-07 13:35:51
Maintainer
Ulrich Wittelsbuerger <ulrich.wittelsbuerger@uni-duesseldorf.de>
License
GPL (>= 2)
Version
0.9.4

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