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WhopGenome (version 0.9.4)

High-Speed Processing of VCF, FASTA and Alignment Data

Description

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.

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Version

Install

install.packages('WhopGenome')

Monthly Downloads

73

Version

0.9.4

License

GPL (>= 2)

Maintainer

Ulrich Wittelsbuerger

Last Published

July 7th, 2016

Functions in WhopGenome (0.9.4)

Close Tabix-indexed file

Extract a part of a FASTA sequence.

Compress file with bgzip

Extract a part of a FASTA sequence.

Open a faidx-indexed FASTA file

Reopen a FAIhandle that has become stale.

Closes a file previously opened with fai_open

Build a tabix index file for fast access to tab-separated-value formatted files.

Build a .fai-index for the given FASTA file.

tabix_getregion

Return the currently selected region of the given tabix file.

tabix_setregion

Reopen a Tabix-indexed file if the filehandle became invalid.

Add a condition for SNP filtering from VCF files.

vcf_clearfilters

Removes all filter steps.

Read a line from a tabix_open()'ed file

Reopen a Tabix-indexed file if the filehandle became invalid.

Open Tabix-indexed file for subsequent access with other tabix_ methods

Build Tabix-index required for processing VCF files.

Close a VCF file previously opened with vcf_open.

tabix_restartregion

Reset the currently selected region to the beginning.

Count how many entries in the selected region

vcf_getcontignames

Return the contig/chromosome identifiers used in the VCF file

Determines whether the last vcf_parse-call returned a SNP (instead of InDel)

vcf_describefilters

Prints description of current filter rules

Get description of currently selected chromosomal region.

vcf_getheaderline

Return one of the header lines of the VCF file

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

Determines whether the last vcf_parse-call returned a InDel (instead of SNP)

vcf_getfieldnames

Return a vector with the field names used in the VCF file.

vcf_readLineVec

Read a line of data from the given VCF file and return the fields as vector elements

vcf_readLineRaw

Read a line of data from the given VCF file and return it as a string without postprocessing.

Reopen a closed or stale VCF file handle.

vcf_parseNextSNP

Read until next SNP or next line and buffer it

vcf_rule.disable

Disable and enable processing of a rule

VCF_read_snp_diplo_bial_int_altpresence

(OBSOLETE) Read batch of biallelic SNP data into matrices

vcf_rule.setcolumn

Set column a rule should examine.

vcf_rule.setaction

Sets the kind of action to take when a rule matches (or does not match).

vcf_restartregion

Let subsequent read calls return from the start of the currently set region.

Read a line of data from the given VCF file and return it as a data frame

Returns whether a VCF file handle is valid and usable.

vcf_selectsamples

Set or query the active sample selection for a given VCF file or get the entire list of individuals.

whop.eg.abbrevForOrganism

Look up the organism prefix for the .org.eg.db databases from Bioconductor

vcf_rule.setfield

Set field or key of filtering rule.

vcf_rule.setcomparison

Set comparison operation for filtering rule.

vcf_rule.setrefvalues

Set reference values for a filtering rule's comparison operation.

whop.eg.chromosome

Return the chromosome on which the gene identified by the given Entrez ID lies.

Set region from which to return genome variation data.

VCF_snpmat_diplo_bial_geno_filtered

Read SNP matrices in one of various representations.

whop.eg.eg_lookup

Return all entries in an EG organism's data table for all given identifiers

whop.eg.fromEnsemblTrans

Turn an Ensemble transcript identifier into a Entrez identifier.

whop.eg.fromOmim

Turn an OMIM identifier into a Entrez identifier.

Open the specified VCF file and return a filehandle for subsequent access.

whop.eg.fromAccnum

Turn a GenBank accession number into a Entrez identifier.

whop.eg.fromPath

Turn a KEGG pathway identifier into related Entrez identifiers.

whop.eg.fromEnzyme

Turn an Enzyme nomenclature identifier into a Entrez identifier.

Look up the start and end of the gene identified by the given Entrez ID.

whop.eg.orgdb_loaded

Find out whether a certain organism's Bioconductor EG database has been loaded

whop.eg.fromAlias

Turn an Alias into a Entrez identifier.

whop.eg.toRefseq

Look up the Refseq identifier(s) corresponding to an Entrez identifier

Look up the Uniprot identifier(s) corresponding to an Entrez identifier

whop.ped.familyOf

Returns all members of an individuals family

Load a GO term database from file

whop.ped.entriesOf

Return all entries from a pedigree dataset matching the list of given identifiers.

whop.go.is_obsolete_byname

Check obsolescence of GO terms with similar names

whop.ucsc.genesForRegion

Return a list of genes located in a certain region on a certain chromosome

whop.ucsc.geneInfoSimilar

Return information UCSC has about any genes with similar names

whop.ucsc.query

Send a SQL query string to the UCSC Genome Browser SQL server

WhopGenome-package

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

whop.eg.fromEnsemblProt

Turn an Ensembl Protein identifier into a Entrez identifier.

whop.eg.fromEnsembl

Turn an Ensembl identifier into a Entrez identifier.

whop.eg.genename

Find the gene name for a given Entrez identifier

Returns GO term identifiers related to the given Entrez identifier.

Look up for an Entrez identifier the corresponding GO terms.

whop.eg.eg_lookupAll

Return all entries in an EG organism's data table for a given identifier

whop.go.term_children

Return child terms of the given term

whop.eg.toEnzyme

Look up for an Entrez identifier the corresponding Enzyme identifiers.

whop.go.term_ancestors

Returns all ancestors of the given GO term.

whop.eg.installdb

Download and install the Bioconductor EG database for a given organism

whop.eg.eg_lookupSingle

Return the first entry in an EG organism's data table for a given 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.load_orgdb

Load and, if necessary, install a Bioconductor EG database for a given organism.

whop.go.term_ancestors_similar

Return ancestral GO terms of similarly named GO term.

Look up the Pathway identifier(s) corresponding to an Entrez identifier

Return all GO terms matching the given one

whop.eg.Organism

Returns the organism's name for which the current database-set contains information.

Look up the OMIM identifier(s) corresponding to an Entrez identifier

whop.eg.fromPmid

Turn an PMID identifier into a Entrez identifier.

Turn an Enzyme identifier into a Entrez identifier.

whop.eg.eg_RevLookup

Perform a reverse lookup on one of the EG organism database's sub-tables.

whop.eg.fromRefseq

Turn a Refseq identifier into a Entrez identifier.

whop.eg.toUniprot

Look up the Uniprot identifier(s) corresponding to an Entrez identifier

whop.eg.toEnsembl

Look up for an Entrez identifier the corresponding Ensembl identifiers.

whop.eg.toAlias

Look up the corresponding common alias for an Entrez identifier.

whop.eg.toUnigene

Look up the Unigene identifier(s) corresponding to an Entrez identifier

whop.ped.females

Return all females from a pedigree dataset

Return only the male individuals from a pedigree dataset

whop.ped.fathers

Return all fathers from a pedigree dataset

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.ped.mothers

Get all mothers stored in a pedigree file

whop.eg.keggpathways

Look up KEGG pathway identifiers related to the given Entrez identifier.

Get all individual names

Load a pedigree dataset from a .PED file

whop.ped.sonsOf

Returns all sons of the given individuals

whop.ped.fromPop

Return all individuals belonging to a given population

whop.ped.parentsOf

Return the parents of individuals

whop.ucsc.geneInfo

Return information from UCSC about a gene named precisely as specified

whop.go.connect

Establish a connection to the AmiGO database servers

whop.go.all_genes_for_term

Returns all genes related to the given GO 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.eg.fromGO2AllEgs

Return all Entrez identifiers related to a given GO term.

whop.eg.selectOrganism

Select the organism to query with subsequent whop.eg calls and load the appropiate database(s).

Turn a GO term identifier into a related Entrez identifier.

whop.go.term_synonyms

Returns GO terms synonymous with the given term

whop.eg.toAccnum

Look up for an Entrez identifier the corresponding GenBank Accession number.

whop.eg.toEnsemblTrans

Look up for an Entrez identifier the corresponding Ensembl transcript identifiers.

whop.go.terms_match

Returns all terms with names similar to the given one.

whop.eg.toEnsemblProt

Look up for an Entrez identifier the corresponding Ensembl Protein identifiers.

Save pedigree data to file

whop.ped.siblingsOf

Return list of siblings