neighborGeneFinder {annotate}R Documentation

A widget for locating genes neighboring a target gene


Given a set of data (matrix) with entries for LocusLink or UniGene ids, the neighboring genes of a gene selected from a list on the interface can be located.


neighborGeneFinder(geneData, keyName = c("unigene", "locuslink"),
organism = c("human", "mouse", "rat")) 


geneData geneData a matrix with columns named. The name for one of the columns has to be either "locuslink" or "unigene"
keyName keyName a character string for the name of the key columns of geneData. Has to be either "locuslink" or "unigene"
organism organism a character string for the name of the organism of interest. Has to be "human", "mouse", or "rat"


Bioconductor's data package XXXCHRLLOC has to be instatlled for the widget to work. If keyName is "unigene", XXXLLMappings is required, where XXX is the name of the organism of interest.


This function returns a list of lists. Elements of the top level list are either LocusLink or UniGene ids. A sublist is inturn a list of lists whose top level elements are chromosome numbers, each of which is a list with an "upstream" and "downstream" elements.


This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R


Jianhua Zhang


     require("annotate", character.only = TRUE) ||
     stop("Package annotate is not availble")
     geneData <- cbind(paste("100", 1:16, "_at", sep = ""), c(1, 50,
                       10044, 51, 71, 51371, 81, 51426, 188, 293, 360,
                       364, 375, 387, 513, 10572))
     colnames(geneData) <- c("Probe", "locuslink")
     neighborGeneFinder(geneData, "locuslink", "human")

[Package annotate version 1.8.0 Index]