vsbuffalo

My message:
This was tweeted recently by an R user, and after trying to figure out why this is, I am stumped:
> a <- 5; b <- 1; c <- 4
> f <- function (n) for (i in 1:n) d <- 1/{a*{b+c}}
> g <- function (n) for (i in 1:n) d <- 1/(a*(b+c))
> system.time(f(1000000))
 user  system elapsed
 3.92    0.00    3.94
> system.time(g(1000000))
 user  system elapsed

vsbuffalo

tracked <- new.env()

makeCounted <- function(fun, loud=FALSE) {
  assign(fun, TRUE, envir=tracked)
  calls <- 0
  countedFun <- function(...) {
    calls <<- .Primitive('+')(1, calls)
    if (loud)
      cat('call made to:', fun, '\n')
    .Primitive(fun)(...)

vsbuffalo

a <- list(id=242, 'session_id'='ah876fh3', main='page.html')

makeURL <-
# Given a named list of key/values, concatenate to make a URL. The
# value of the entry with key 'main' is treated as the HTML page.
function(pieces) {
  m <- which(names(pieces) == 'main')
  keys.values <- paste(names(pieces[-m]), pieces[-m], collapse='&', sep='=')
  return(paste(pieces[[m]], keys.values, sep='?'))
}

vsbuffalo

d <- local({
    s <- apply(obj$qual.freqs[, -1], 1, binsample)
    tmp <- t(s)
    nr <- nrow(tmp)
    dim(tmp) <- c(ncol(tmp)*nrow(tmp), 1)
    tmp <- as.data.frame(cbind(1:nr, tmp))    
    colnames(tmp) <- c('position', 'quality')
    return(tmp)
})

vsbuffalo

# R package Makefile template
# Vince Buffalo <[email protected]> (with poly-A tail removed)
#
# Replace 'package' with the name of your package (which should be a
# directory). My layout for package development is:
# package_build
#  - TODO
#  - Readme.md (for Github)
#  - package (actual R package directory)
#  - Makefile (this)

vsbuffalo

# If you have a long vector of integers to compare against an integer literal, 
# specify that the numerical literal is an integer rather than letting
# R coerce the entire vector to doubles. 
x <- as.integer(floor(rnorm(1000000, 0, 1000)))

system.time(x < 0)
#   user  system elapsed 
#  0.014   0.000   0.014 

system.time(x < 0L)

vsbuffalo

## Vince Buffalo's .profile

## Some fun first:
curl --connect-timeout 1 -Is slashdot.org | egrep '^X-(F|B)' | sed 's/^X-//'

## Set environmental variables
export PATH=/opt/local/bin:/opt/local/sbin:/usr/local/bin/:$PATH
export CLICOLOR=1
export EDITOR="emacsclient"
export LSCOLORS="gxfxcxdxbxegedabagacad"

vsbuffalo

shell -$SHELL
startup_message off
defscrollback 30000
autodetach on
hardstatus on
hardstatus alwayslastline
altscreen on

screen -t irc 0 /opt/local/bin/irssi

vsbuffalo

;; From Michael Hannon and Vince Buffalo

(require 'cl)

(defun flatten (list)            ; From `misc-fns.el'.                                                                                                                                                                               
  "Flatten LIST, returning a list with the atoms in LIST at any level.                                                                                                                                                               
  Also works for a consp whose cdr is non-nil.                                                                                                                                                                                                                                                                                                                                                                                                               
  Borrowed from: http://www.emacswiki.org/emacs/lib-requires.

vsbuffalo

## analysis.R -- looking at how similar the results of edgeR and DESeq are                                                                                   
## [email protected] sans poly-A tail                                                                                                                 


library(pasilla)
library(DESeq)
library(edgeR)
library(ggplot2)
library(limma)