Gaggle Components
Geese
Data Standards
Boss

Using the Gaggle R Package

If you have not already installed the R goose, please read the installation instructions.

Startup

  1. Start R (if it is not already running).
  2. At the R prompt, type these commands:
    
    library(gaggle)
    gaggleInit()
    source("http://gaggle.systemsbiology.net/R/gaggleUtil.R")
    

    You can put those lines in a file called .Rprofile in your home directory. This will cause R to connect to Gaggle every time it is started. You can find your home directory by issuing this command in R:

    Sys.getenv("R_USER")
    
  3. For a simple test:
     showGoose ('boss') 
    You will see the Gaggle Boss appear.
  4. For more detail and examples, please examine this vignette, or examine the scenarios listed in the cribsheet.

Receive

After successful initialization, gaggle matrix and name list broadcasts are available in your R console via these commands:


  myMatrix <- getMatrix () 
  
      or
myList <- getNameList ()

In each case, the most recently broadcasted matrix or name list will be returned.

broadcast

Broadcast a matrix or a list of names to the gaggle.


  broadcast (matrix1)    
  broadcast (matrix2, "my matrix")
  broadcast (transpose (matrix3), "transposed matrix")
  nameList = c ("VNG0101G", "VNG0177G", "VNG0286C")
  broadcast (nameList)

related commands

  • get the names of all current geese:
    geese ()
  • all subsequent broadcasts go to this goose (use 'boss' for multi-casts):
    setTargetGoose (gooseName)
  • find out what the current goose is:
    getTargetGoose ()
© 2006, Institute for Systems Biology, All Rights Reserved
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