High-Speed Processing of VCF, FASTA and Alignment Data


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Documentation for package ‘WhopGenome’ version 0.9.7

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B F R T V W

WhopGenome-package High-speed, high-specialisation population-scale whole-genome variation and sequence data access

-- B --

bgzf_compress Compress file with bgzip

-- F --

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_query3 Extract a part of a FASTA sequence.
fai_query4 Extract a part of a FASTA sequence.
fai_query5 Extract a part of a FASTA sequence.
fai_reopen Reopen a FAIhandle that has become stale.

-- R --

read_snp_diplo_bial_int_altpresence Read SNP matrices in one of various representations.
read_snp_diplo_bial_int_nuclcodes Read SNP matrices in one of various representations.
read_snp_diplo_bial_str_01 Read SNP matrices in one of various representations.
read_snp_diplo_bial_str_allelechars Read SNP matrices in one of various representations.
read_snp_diplo_bial_str_nuclcodes Read SNP matrices in one of various representations.

-- T --

tabix_build Build a tabix index file for fast access to tab-separated-value formatted files.
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_ methods
tabix_read Read a line from a tabix_open()'ed file
tabix_readraw 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.

-- V --

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_countBiallelicSNPs Count how many entries in the selected region
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 read.
vcf_getAlt Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getChrom Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
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_getFilter Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getFormat Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getheaderline Return one of the header lines of the VCF file
vcf_getID Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getInfo Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getInfoField Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getnumcontigs Get the number of different contigs/chromosomes stored in the file
vcf_getPos Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getQual Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getRef Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getregion Get description of currently selected chromosomal region.
vcf_getSample Return a specific piece of information from the last line processed with vcf_parseNextSNP or vcf_parsenextline.
vcf_getsamples Set or query the active sample selection for a given VCF file or get the entire list of individuals.
vcf_getselectedsamples Set or query the active sample selection for a given VCF file or get the entire list of individuals.
vcf_isINDEL Determines whether the last vcf_parse-call returned a InDel (instead of SNP)
vcf_isSNP Determines whether the last vcf_parse-call returned a SNP (instead of InDel)
vcf_open Open the specified VCF file and return a filehandle for subsequent access.
vcf_parseNextLine Read until next SNP or next line and buffer it
vcf_parseNextSNP Read until next SNP or next line and buffer it
VCF_readIntoCodeMatrix Read SNP matrices in one of various representations.
vcf_readLineDF Read a line of data from the given VCF file and return it as a data frame
vcf_readLineRaw Read a line of data from the given VCF file and return it as a string without postprocessing.
vcf_readLineRawFiltered Read a line of data from the given VCF file and return it as a string without postprocessing.
vcf_readLineVec Read a line of data from the given VCF file and return the fields as vector elements
vcf_readLineVecFiltered Read a line of data from the given VCF file and return the fields as vector elements
VCF_read_snp_diplo_bial_int_altpresence (OBSOLETE) Read batch of biallelic SNP data into matrices
VCF_read_snp_diplo_bial_int_nuclcodes (OBSOLETE) Read batch of biallelic SNP data into matrices
VCF_read_snp_diplo_bial_str_01 (OBSOLETE) Read batch of biallelic SNP data into matrices
VCF_read_snp_diplo_bial_str_allelechars (OBSOLETE) Read batch of biallelic SNP data into matrices
VCF_read_snp_diplo_bial_str_nuclcodes (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 currently set region.
vcf_rule.disable Disable and enable processing of a rule
vcf_rule.enable Disable and enable processing of a rule
vcf_rule.setaction Sets the kind of action to take when a rule matches (or does not match).
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 operation.
vcf_selectsamples Set or query the active sample selection for a given VCF file or get the entire list of individuals.
vcf_setregion Set region from which to return genome variation data.
VCF_snpmat_anyplo_anyal_nucodes_filtered Read SNP matrices in one of various representations.
VCF_snpmat_anyplo_anyal_nucodes_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_anyplo_bial_nucodes_filtered Read SNP matrices in one of various representations.
VCF_snpmat_anyplo_bial_nucodes_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_anyal_geno_filtered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_anyal_geno_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_anyal_hasalt_filtered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_anyal_hasalt_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_anyal_ishet_filtered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_anyal_ishet_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_anyal_nucodes_filtered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_anyal_nucodes_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_bial_geno_filtered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_bial_geno_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_bial_hasalt_filtered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_bial_hasalt_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_bial_ishet_filtered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_bial_ishet_unfiltered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_bial_nucodes_filtered Read SNP matrices in one of various representations.
VCF_snpmat_diplo_bial_nucodes_unfiltered Read SNP matrices in one of various representations.
vcf_valid Returns whether a VCF file handle is valid and usable.

-- W --

whop.eg.abbrevForOrganism Look up the organism prefix for the .org.eg.db databases from Bioconductor
whop.eg.chromosome Return the chromosome on which the gene identified by the given Entrez ID lies.
whop.eg.eg_lookup Return all entries in an EG organism's data table for all given identifiers
whop.eg.eg_lookupAll Return all entries in an EG organism's data table for a given identifier
whop.eg.eg_lookupSingle Return the first entry in an EG organism's data table for a given identifier
whop.eg.eg_RevLookup Perform a reverse lookup on one of the EG organism database's sub-tables.
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 identifier.
whop.eg.fromEnzyme Turn an Enzyme nomenclature identifier into a Entrez identifier.
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 identifiers.
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 identifier.
whop.eg.installdb Download and install the Bioconductor EG database for a given organism
whop.eg.keggpathways Look up KEGG pathway identifiers related to the given Entrez identifier.
whop.eg.load_orgdb Load and, if necessary, install a Bioconductor EG database for a given organism.
whop.eg.Organism Returns the organism's name for which the current database-set contains information.
whop.eg.orgdb_loaded Find out whether a certain organism's Bioconductor EG database has been loaded
whop.eg.region Look up the start and end of the gene identified by the given Entrez ID.
whop.eg.selectOrganism Select the organism to query with subsequent whop.eg calls and load the appropiate database(s).
whop.eg.toAccnum Look up for an Entrez identifier the corresponding GenBank Accession number.
whop.eg.toAlias Look up the corresponding common alias for an Entrez identifier.
whop.eg.toEnsembl Look up for an Entrez identifier the corresponding Ensembl identifiers.
whop.eg.toEnsemblProt Look up for an Entrez identifier the corresponding Ensembl Protein identifiers.
whop.eg.toEnsemblTrans Look up for an Entrez identifier the corresponding Ensembl transcript identifiers.
whop.eg.toEnzyme Look up for an Entrez identifier the corresponding Enzyme identifiers.
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 identifier
whop.eg.toPath Look up the Pathway identifier(s) corresponding to an Entrez identifier
whop.eg.toPmid Look up the Uniprot identifier(s) corresponding to an Entrez identifier
whop.eg.toRefseq Look up the Refseq identifier(s) corresponding to an Entrez identifier
whop.eg.toUnigene Look up the Unigene identifier(s) corresponding to an Entrez identifier
whop.eg.toUniprot Look up the Uniprot identifier(s) corresponding to an Entrez identifier
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 the given one
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.terms_match Returns all terms with names similar to 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.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 dataset
whop.ped.entriesOf Return all entries from a pedigree dataset matching the list of given identifiers.
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
whop.ucsc.geneInfo Return information from UCSC about a gene named precisely as specified
whop.ucsc.geneInfoSimilar Return information UCSC has about any genes with similar names
whop.ucsc.genesForRegion Return a list of genes located in a certain region on a certain chromosome
whop.ucsc.query Send a SQL query string to the UCSC Genome Browser SQL server
WhopGenome High-speed, high-specialisation population-scale whole-genome variation and sequence data access