neighborGeneFinder {annotate} | R Documentation |
Given a set of data (matrix) with entries for Entrez Gene 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 |
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keyName |
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organism |
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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 Entrez Gene 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.
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") }