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

#' Modified version of the ggplot2 plotmatrix function that accepts additional
#' variables for aesthetic mapping.
#' 
#' example
#' data(iris)
#' iris.vars <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")
#' ggpairs(data = iris, facet.vars = iris.vars, 
#'  mapping = aes(color = Species, shape = Species))

ggpairs <- function (data, facet.vars = colnames(data), facet.scale = "free",

aaronwolen

# Code written by brentp in response to BioStars question:
# http://www.biostars.org/post/show/6544/

import random
import sys

def write_random_records(fqa, fqb, N=100000):
    """ get N random headers from a fastq file without reading the
    whole thing into memory"""
    records = sum(1 for _ in open(fqa)) / 4

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

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

% Title % Name % Date

My first slide

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