jokergoo

bedtools = function(cmd, envir = parent.frame()) {
	gr = gsub("^.*@\\{(.*?)\\}.*$", "\\1", cmd)
	gr = get(gr, envir = envir)
	file = tempfile(fileext = ".bed")
	write.table(gr, file = file, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE)
	cmd = gsub("@\\{.*?\\}", file, cmd)
	try(tb <- read.table(pipe(cmd), stringsAsFactors = FALSE))
	file.remove(file)
	return(tb)
}

jokergoo

set_module = function(module) {
	assign("__module__", module, envir = parent.frame())
}

load_module = function(file) {
	
	e = new.env()
	source(file, local = e, verbose = FALSE)
	module = get("__module__", envir = e)
	rm(e)

jokergoo

is_abs_unit <- function(x) UseMethod("is_abs_unit")

is_abs_unit.unit = function(x) {
	unit = attr(x, "valid.unit")
	if(unit %in% c(1:4, 7:24)) {
		return(TRUE)
	} else {
		return(FALSE)
	}

jokergoo

require(RColorBrewer)
 
 
# since gene expression data always contains a lot of samples.
# If one want to see distributions of samples, using boxplot would be not so clear.
# The function use continuous colors to represent density distributions of expression
# values in samples and can make a better illustration of the data.
heatplot = function(x, col=rev(brewer.pal(10, "Spectral")), draw.quantiles = TRUE, align = TRUE, each = FALSE, ...) {
    if(is.vector(x) && class(x) != "list") {
        x = as.matrix(x)

jokergoo

color.pal = function(x, col = c("green", "black", "red"), breaks = c(-5, 0, 5)) {
    
    if(length(col) != length(breaks)) {
		stop("Length of col should be equal to the length of breaks.\n")
	}
	
    # change col represented as strings to RGB space
    col_section = sapply(col, function(x) as.vector(col2rgb(x)))
    col_section = t(col_section)
    

jokergoo

# == title
#   Simple template for text interpolation
#
# == description
#   I like text interpolation in Perl. But in R, if you want to connect plain text and variables,
# you need to use `paste` or functions in `stringr`. However, if there are so many variables or 
# or many quotes in the string you want to construct, it would be a little terrible.
#   So, this function allows you to construct strings as Perl style.
#
# == param

jokergoo

assignment = function(x, k = 4) {
	
	names(x) = seq_along(x)
	
	y = vector("list", k)
	ysum = sapply(y, function(x) 0)
 
	flag = 0
	while(length(x)) {
		if(flag) {

jokergoo

build.position.index = function(x, by = 5) {
	
	segment = round((x/(10^by)))*10^by 
	se = unique(segment)
	mat = matrix(nrow = length(se), ncol = 2)
	for(i in seq_along(se)) {
		mat[i, ] = range(which(segment == se[i]))
	}
	list(mat = mat, segment = se, by = 10^by)
}

jokergoo

var unread = new Array();
var checked = new Array();
var from = new Array();
var subject = new Array();
var rows = new Array();

load_all = function() {
	rows = document.getElementsByClassName("lvm")[0].lastChild.childNodes;

jokergoo

Path of SRA files:

http://sra-download.ncbi.nlm.nih.gov/srapub/SRR\\d+