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

## Documentation for package ‘NCBI2R’ version 1.4.4

- DESCRIPTION file.
- Code demos. Use demo() to run them.

## Help Pages

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
CompareTaxInfo | Identify common lineages of taxonomy terms
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
GenomeSort | Sorts the genome by chromosome and position
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.
GetGenesInSNPs | Returns a vector of genes that the provided SNPs are located within.
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
GetPublishedGWAS | Obtains published GWAS association values
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
GetTaxInfo | Get Taxonomy information
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).