neighborGeneFinder {annotate} | R Documentation |
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
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") }