lgatto

library(MSnbase)
n <- 10000
ll <- vector("list",length=n)
e <- new.env()
tl <- system.time(for (i in 1:n)
                  ll[[i]] <- new("Spectrum2"))
te <- system.time(for (i in 1:n)
                  assign(paste("X",i,sep=""),new("Spectrum2"),e))

## Results for n=10000

lgatto

m <- matrix(runif(1e6),nrow=10000)

## append to result vector -- slow
res1 <- NULL
t1 <- system.time(for (i in 1:1000) res1[i] <- sum(m[i,]))

## initialise to full length -- fast
res2 <- numeric(1000)
t2 <- system.time(for (i in 1:1000) res2[i] <- sum(m[i,]))

lgatto

## Credit Hadley Wickham 
## http://www.mail-archive.com/r-help@r-project.org/msg125980.html
watch <- function(varname) {
 old <- get(varname)
 changed <- function(...) {
   new <- get(varname)
   if (!identical(old, new)) {
     message(varname, " is now ", new)
     old <<- new
   }

lgatto

##' Return the name of variable \code{varname} in call \code{match_call}.                                                                             
##'                                                                                                                                                   
##' @title Return a variable name                                                                                                                     
##' @param match_call An object of class \code{call}, as returned by \code{match.call}.                                                               
##' @param varname An \code{character} of length 1 which is looked up in \code{match_call}.                                                           
##' @return A \code{character} with the name of the variable passed as parameter                                                                      
##' \code{varname} in parent close of \code{match_call}.                                                              

lgatto

scatterhist <- function(x, y, xlab="", ylab="", ...){
  zones <- matrix(c(2,0,1,3), ncol=2, byrow=TRUE)
  layout(zones, widths=c(4/5,1/5), heights=c(1/5,4/5))
  xhist <- hist(x, plot=FALSE)
  yhist <- hist(y, plot=FALSE)
  top <- max(c(xhist$counts, yhist$counts))
  par(mar=c(3,3,1,1))
  plot(x,y, ...)
  par(mar=c(0,3,1,1))
  barplot(xhist$counts, axes=FALSE, ylim=c(0, top), space=0)

lgatto

> library(kernlab)
> data(iris)
> irismodel1 <- ksvm(Species ~ ., data = iris)
Using automatic sigma estimation (sigest) for RBF or laplace kernel 
> irismodel2 <- ksvm(Species ~ ., data = iris)
Using automatic sigma estimation (sigest) for RBF or laplace kernel 
> table(predict(irismodel1, iris[,-5]), predict(irismodel2, iris[,-5]))
            
             setosa versicolor virginica
  setosa         50          0         0

lgatto

## http://gettinggeneticsdone.blogspot.co.uk/2012/09/deseq-vs-edger-comparison.html

library(DESeq)
library(edgeR)
library(VennDiagram)

# Read in data ------------------------------------------------------------

## Use pasilla data
datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )

lgatto

getDependencies <- function(p,
                            rep = c("BioCsoft", "BioCann", "BioCexp", "BioCextra", "CRAN"),
                            biocVersion = "2.12",
                            depLevels = c("Depends", "Imports", "Suggests"),
                            filter = TRUE) {
  rep <- match.arg(rep)
  if (rep == "CRAN") {
    rep <- getOption("repos")["CRAN"]
  } else {
    biocMirror <- getOption("BioC_mirror", "http://bioconductor.org")

lgatto

library(base64enc)
library(RJSONIO)
library(httr)

default_key <- function () {
  key <- Sys.getenv("POSTMARKAPP_API_KEY")
  if (key == "") {
    stop("Either provide key or set envvar POSTMARKAPP_API_KEY", call. = FALSE)
  }
  key

lgatto

;; grep -h X-Key */*/cur/* | sed -e 's/X-Keywords: //; s/, /\n/g' | sort | uniq > xkeys.txt

(setq mu4e-xkeys "~/Maildir/xkeys.txt")

(defun read-lines (f)
  "Return a list of lines of a file at f."
  (with-temp-buffer
    (insert-file-contents f)
    (split-string (buffer-string) "\n" t)))