neighborGeneFinder {annotate} | R Documentation

## A widget for locating genes neighboring a target gene

### Description

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.

### Usage

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

### Arguments

`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"

### Details

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.

### Value

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.

### Note

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

### Author(s)

Jianhua Zhang

### Examples

      if(interactive()){
         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")
      }

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