aaronwolen

```{r}
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))))

aaronwolen

# dataframetools
# A few simple functions for performing simple tasks with data.frames
# ---
# Includes functions for:
# 
# - reordering data.frames
# - identifying invariant or blank columns
# - identifying groups of columns that are redundant with each other
# - converting all columns of class factor to class character

aaronwolen

#' Generate data.frame of feature annotations
#' 
#' Use bioconductor annotation packages to create a data.frame of feature/probe
#' annotations.
#' 
#' @param chip character string identifying chip model (e.g., "illuminaHumanv2")
#' @param features optional character vector of chip features (i.e., probeset ids)
#' @param vars character vector of desired annotations. These must match objects
#'   provided by the annotation package (e.g., "CHR")
#' @param duplicate.values how should duplicate values be handled? The default

aaronwolen

#' FTP tree mapper
#' Save an FTP site's directory stucture as a list.
#' @author Aaron Wolen
#' 
#' @example
#' url <- 'ftp://ftp.genboree.org/EpigenomeAtlas/Current-Release/experiment-sample' 
#' roadmap <- map_ftp(url = url, dirs = "Histone_H2BK120ac", recursive = TRUE)

map_ftp <- function(url, dirs, recursive = FALSE) {
  require(RCurl, quietly = TRUE)

aaronwolen

aaronwolen

library(IRanges)
library(GenomicRanges)
library(rtracklayer)

# Select a BigWig file
bw.dir <- "/home/chromatin/roadmap/DNase_hypersensitivity/brain_fetal"
bw.file <- dir(bw.dir, full.names = TRUE, pattern = "*.bigWig")[1]

# Specify a genomic range
selection <- GRanges(seqnames = "chr4",

aaronwolen

install.packages(c("RCurl", "XML"))

bioc.v <- tools:::.BioC_version_associated_with_R_version
repos <- tools:::.read_repositories(file.path(R.home("etc"), "repositories"))

bioc.repo <- repos["BioCsoft",]$URL
bioc.repo <- sub("2\\.\\d+", bioc.v, bioc.repo)

packages <- c("zlibbioc", "BiocGenerics", "Biobase", "IRanges", 
  "AnnotationDbi", "GenomicRanges", "Biostrings", "Rsamtools", 

aaronwolen

#!/bin/bash

# Partially convert Rnw presentations to Rmd syntax
# - [x]: Code chunks
# - [x]: Section headers
# - [x]: Slide headers
# - [x]: Presenter notes
# - [x]: Lists
# - [ ]: Inlinde code (sort of, not really)

aaronwolen

clipboard <- function(x, sep.lines = FALSE){
  clipboard <- pipe('pbcopy', 'w')
  
  if(sep.lines){
    x <- unlist(strsplit(as.character(x), split = ","))
    x <- sub(" ", "", x)
  }
  
  write.table(x, clipboard, sep = "\t", 
    quote = FALSE, col.names = FALSE, row.names = FALSE)

aaronwolen

1. Open the "Template Files" pane in BibDesk's preferences
2. Use the "+" button to add a new general template
3. Double click the red text and choose citeServiceTemplateMD.txt
4. Open the "Citation" pane in BibDesk's preferences
5. Change "Default format" to "Template"
6. Change "Template" to "citeServiceTemplateMD"