gauthamnair

//--

// Clojure's Transducers

// (the simpler parts)


//--

// References:

gauthamnair

package code

object Process0 {
	sealed trait Process[I, O] {
    import Process._
    def |>[O2](p2: Process[O,O2]): Process[I,O2] = compose(this, p2)
    def ++(p2: Process[I,O]): Process[I,O] = concat(this, p2)
    def flatMap[O2](f: O => Process[I,O2]): Process[I,O2] = nest(this)(f)
  }

gauthamnair

Instructions: you would have to download and format the Marks et al. data from 
their supplement first. Then, save this file as an .Rnw, Stangle and 
source the resulting .R file. 


Import data from Marks et al. Cell 2012. 
<<>>=
dat <- read.table('./marks2i.serum.example.txt')
# > head(dat)
#      GeneSymbol   log2Fold pval

gauthamnair

% Instructions: Save as .Rnw, run Stangle in an R session and source the resulting .R file.
% Some required libraries: data.table, GO.db, stringr

A helper function to exclude GO terms that are too small or too big, as measured by the number or genes annotated for it.
<<>>=
require(data.table)
f.GOsizefilter <- function( gotable, gosizecutoff=250, keepsmaller = TRUE ){
    # gotable: One column is Category, another is GeneSymbol. 
    # One row for every Category that contains the gene
    gotable <- as.data.table(gotable)