Collate Gene Annotation Data from Uniprot and NIH Gene Databases


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Documentation for package ‘ungeneanno’ version 0.1.6

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ungeneanno-package Collate Gene Annotation Data from Uniprot and NIH Gene Databases
gene An S4 class to represent a gene.
gene-class An S4 class to represent a gene.
geneanno An S4 class to represent the base information used by the methods.
geneanno-class An S4 class to represent the base information used by the methods.
genematrix Input Matrix of Drug/Gene Data
getGeneSummary Create gene specific objects containing data from online resources
getGeneSummary-method Create gene specific objects containing data from online resources
getGroupGeneList Create unique list of group,gene combinations from input list
getGroupGeneList-method Create unique list of group,gene combinations from input list
getNihQuery create initial NIH Query
getNihQuery-method create initial NIH Query
getNihSummary Gather NIH Gene Data
getNihSummary-method Gather NIH Gene Data
getPublicationList Gather NIH Pubmed Data
getPublicationList-method Gather NIH Pubmed Data
getUniprotSummary Gather Uniprot Data
getUniprotSummary-method Gather Uniprot Data
getUniqueGeneList Create unique list of genes from input list
getUniqueGeneList-method Create unique list of genes from input list
inputlist Input Vector of Drug/Gene Data
parseInputFile Parse files of gene names and group identifiers to create unique lists of each
parseInputFile-method Parse files of gene names and group identifiers to create unique lists of each
produceOutputFiles Save Gene Information to group Specific Output Files
produceOutputFiles-method Save Gene Information to group Specific Output Files
pubmed An S4 class to represent a query to the Pubmed database, inherits from 'geneanno' class.
pubmed-class An S4 class to represent a query to the Pubmed database, inherits from 'geneanno' class.
query An S4 class to represent an initial query to the NCBI e-utilities, inherits from 'geneanno' class.
query-class An S4 class to represent an initial query to the NCBI e-utilities, inherits from 'geneanno' class.
searchPublications Carry out Pubmed search for a mtrix
searchPublications-method Carry out Pubmed search for a mtrix
ungeneanno Collate Gene Annotation Data from Uniprot and NIH Gene Databases