aaronwolen

# Download the latest GENCODE annotations file and export as a GRanges object
library(RCurl)
library(rtracklayer)


# Variables ---------------------------------------------------------------

# 'human' or 'mouse'
organism <- "human"

aaronwolen

library(ggplot2)
library(plyr)


# Load data ---------------------------------------------------------------

enrich.file <- "results/alspac/enrichment/enrichment-results-alspac-encode-dnase-h3k4me3.csv"
enrich.df <- read.csv(enrich.file, stringsAsFactors = FALSE)

# address stem-cell samples missing tissue annotation

aaronwolen

javascript:var%20insert_proxy%20=%20function(proxy)%20{var%20url%20=%20document.URL;if%20(url.indexOf(proxy)%20===%20-1)%20{var%20parser%20=%20document.createElement(%27a%27);parser.href%20=%20url;var%20host%20=%20parser.host;if%20(host%20==%20%27www.ncbi.nlm.nih.gov%27)%20{host%20=%20host.replace(/\./g,%20%27-%27);};host%20=%20host.concat(proxy);proxy_url%20=%20url.replace(parser.host,%20host);window.open(proxy_url,%20%27_self%27);};};insert_proxy(%27.proxy.library.vcu.edu%27);

aaronwolen

# Parse pathway file containing entries from the KEGG enzyme, orthology and
# pathway databases. 
#
# For cases when there are multiple matches across databases all combinations
# of the match are returned. For example, some enzyme entries map to multiple
# orthologies:
#
# K00918  ADP-dependent phosphofructokinase/glucokinase [EC:2.7.1.146 2.7.1.147]
#
# will become...

aaronwolen

# Extract and append multiple values embedded in rows
#
# data: data.frame
# col: column name containing embedded values
# sep: regular expression to split column by
#
# df <- data.frame(key = c("a", "a;b", "a;b;c"), val = 1:3)
# unembed(df, "key", ";")

unembed <- function(data, col, sep, ...) {

aaronwolen

# Identify clusters of contiguous factors within a dendrogram
# Aaron Wolen
#
# See http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038422
# for an example situation in which this would be useful
#
# x: dendrogram
# f: a named vector containing the factor that defines the grouping of leaves,
#    must be named using the same values that define x's leaf labels

aaronwolen

---
title: "test"
output:
  html_document:
    keep_md: yes
---

```{r}
library(qtl)
library(qtlcharts)

aaronwolen

(* 
	display-specific fullscreen behavior
	
	enable fullscreen for specific applications on MacBook and disable fullscreen
	when using a larger external display

	adapted from:
	* https://gist.github.com/dsummersl/4175461
	* http://daringfireball.net/2006/12/display_size_applescript_the_lazy_way
*)

aaronwolen

# A few simple rules from Stephen Wolfram's A New Kind of Science

apply_rule <- function(x, rule = "254") {
  stopifnot(length(x) == 3)
  stopifnot(all(x %in% c(0, 1)))
  
  rules <- list("254" = c(1, 1, 1, 1, 1, 1, 1, 0),
                "250" = c(1, 1, 1, 1, 1, 0, 1, 0),
                "90"  = c(0, 1, 0, 1, 1, 0, 1, 0),
                "30"  = c(0, 0, 0, 1, 1, 1, 1, 0))

aaronwolen

library(microbenchmark)

set.seed(1024) nr <- 1e4 nc <- 100

m <- matrix(runif(nr * nc), nrow = nr, dimnames = list(paste0("g", seq_len(nr)), paste0("s", seq_len(nc))))