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")
  }
  

[Package annotate version 1.8.0 Index]