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