NCBI2R-An R package to navigate and annotate genes and SNPs

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Documentation for package ‘NCBI2R’ version 1.3.5

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AdjustRangeAroundGene Adjusts gene position
AminoAcids Reference table of amino acids
AnnotateDataframe Uses NCBI to annotate dataframe
AnnotateSNPFile Annotates SNPs from a file
AnnotateSNPList Annotates SNPs from NCBI
Comp Produces a complementary DNA sequence
ConvertIUPAC Convert IUPAC allele ambiguity abbreviation codes
ConvertProtein Converts between different types of amino acid codes.
ConvertPubMedHeadings Convert MEDLINE abbreviations to descriptions
Delay Pauses the code for N seconds
DelayUntil Pauses the code until a specified time
DivideString Converts a string into fragment pieces based on a comma or other separator
GetARFromLocation Filter your association results.
GetClosestGeneInfo Obtains information about the closest genes to a list of SNPs.
GetGeneInfo Obtains information about genes from NCBI
GetGeneNames Obtains information about user defined genes from NCBI
GetGenesInRegion Use this to find a list of genes in a particular region of the genome.
GetGeneTable get intron/exon data from NCBI
GetGOs Obtains Gene Ontologies from NCBI.
GetIDs Obtain Entrez ID numbers
GetInteractions Obtains interacting genes from NCBI
GetLDInfo Obtain Linkage Disequilibrium (LD) information from HapMap for a given genomic region.
GetNeighGenes Obtains neighbouring genes from NCBI
GetPathways Obtains pathways from NCBI for a given set of genes
GetPhenotypes Obtains pathways from NCBI for a given set of genes
GetPubMed Obtains references from NCBI's PubMed database
GetRegion Use this to find out a list of snps or genes in a particular region of the genome
GetSNPFlankSeq Obtains flanking sequence of a set of SNPs from NCBI
GetSNPInfo Obtains NCBI information about one or more SNPs
GetSNPPosHapMap Get the chromosomal position of any SNP on the HapMap.
GetSNPProxyInfo Obtain proxy SNP information for a given SNP that is in close LD with your requested SNP.
GetSNPsInGenes This function returns a vector of all the SNPs within the boundary of a gene or genes.
GetSNPsInRegion Obtains a list of SNPs in a particular region of the genome.
GetTax Find the NCBI Taxonomy ID number using a search term
GetUniSTSFromName Find information about UniSTS from NCBI
GetUniSTSInfo Obtains information about a given UniSTS from NCBI
GetUniSTSSpecies Obtains a list of species with data for a given UniSTS
gwas Sample gwas data from a fictional project
IUPAC Produces a dataframe of the IUPAC DNA allele ambiguity abbreviation codes
MakeExcel Creates an Excel spreadsheet from genetic information.
MakeHTML Converts genetic annotation dataframes into a HTML document.
MedlineAbbreviations Produces a dataframe of the Medline abbreviations
MergeSNPsGenes Function to merge SNP information and Gene information
NatureJobs Obtains a dataframe of jobs listed on the NatureJobs.com website
OpenPDF Opens an available PDF from the PudMed Central database
OpenPMID Opens the PubMed webpage for a given PMID
OpenURL Opens a webbrowser to a given address.
PrintFilters Displays the list of gene filters available on NCBI.
PrintNCBI2RInfo Displays summary information about NCBI2R.
PrintNCBI2ROptions Displays the options in use by NCBI2R.
RemoveSpaces Removes spaces at the start of a string and the end of a string
Rev Produces a reverse DNA sequence
RevComp Produces a reverse complement DNA sequence
ScanForGenes Filters your association results for those found within a list of genes.
ScanForSNPs Filters your association results for those that match a list of SNPs.
SplitGenes Checks and converts SNP information for multiple genes.
UpdateCheck Checks for a more recent version of NCBI2R
VisualiseRegion Produces a graphical representation of the region, with the exons (optional).