#' Randomly permute the locations of a feature file among a genome.
#'
#' @param i <bed/gff/vcf>
#' @param g <genome>
#' @param excl A BED/GFF/VCF file of coordinates in which features in -i
#' should not be placed (e.g. gaps.bed).
#'
#' @param incl Instead of randomly placing features in a genome, the -incl
#' options defines a BED/GFF/VCF file of coordinates in which
#' features in -i should be randomly placed (e.g. genes.bed).
#' Larger -incl intervals will contain more shuffled regions.
#' This method DISABLES -chromFirst.
#'
#' @param chrom Keep features in -i on the same chromosome.
#' - By default, the chrom and position are randomly chosen.
#' - NOTE: Forces use of -chromFirst (see below).
#'
#' @param seed Supply an integer seed for the shuffling.
#' - By default, the seed is chosen automatically.
#' - (INTEGER)
#'
#' @param f Maximum overlap (as a fraction of the -i feature) with an -excl
#' feature that is tolerated before searching for a new,
#' randomized locus. For example, -f 0.10 allows up to 10 percent
#' of a randomized feature to overlap with a given feature
#' in the -excl file. **Cannot be used with -incl file.**
#' - Default is 1E-9 (i.e., 1bp).
#' - FLOAT (e.g. 0.50)
#'
#' @param chromFirst
#' Instead of choosing a position randomly among the entire
#' genome (the default), first choose a chrom randomly, and then
#' choose a random start coordinate on that chrom. This leads
#' to features being ~uniformly distributed among the chroms,
#' as opposed to features being distribute as a function of chrom size.
#'
#' @param bedpe Indicate that the A file is in BEDPE format.
#'
#' @param maxTries
#' Max. number of attempts to find a home for a shuffled interval
#' in the presence of -incl or -excl.
#' Default = 1000.
#'
#' @param noOverlapping
#' Don't allow shuffled intervals to overlap.
#'
#' @param allowBeyondChromEnd
#' Allow shuffled intervals to be relocated to a position
#' in which the entire original interval cannot fit w/o exceeding
#' the end of the chromosome. In this case, the end coordinate of the
#' shuffled interval will be set to the chromosome's length.
#' By default, an interval's original length must be fully-contained
#' within the chromosome.
#'
#' @param output Output filepath instead of returning output in R.
#'
bt.shuffle <- function(i, g, excl = NULL, incl = NULL, chrom = NULL, seed = NULL, f = NULL, chromFirst = NULL, bedpe = NULL, maxTries = NULL, noOverlapping = NULL, allowBeyondChromEnd = NULL, output = NULL)
{
# Required Inputs
i <- establishPaths(input=i, name="i", allowRobjects=TRUE)
g <- establishPaths(input=g, name="g", allowRobjects=TRUE)
options <- ""
# Options
if(!is.null(excl))
excl <- establishPaths(input=excl, name="excl", allowRobjects=TRUE)
if(!is.null(incl))
incl <- establishPaths(input=incl, name="incl", allowRobjects=TRUE)
options <- createOptions(names=c("excl", "incl", "chrom", "seed", "f", "chromFirst", "bedpe", "maxTries", "noOverlapping", "allowBeyondChromEnd"), values=list(excl, incl, chrom, seed, f, chromFirst, bedpe, maxTries, noOverlapping, allowBeyondChromEnd))
# establish output file
tempfile <- tempfile("bedtoolsr", fileext=".txt")
tempfile <- gsub("\\", "/", tempfile, fixed=TRUE)
bedtools.path <- getOption("bedtools.path")
if(!is.null(bedtools.path)) bedtools.path <- paste0(bedtools.path, "/")
cmd <- paste0(bedtools.path, "bedtools shuffle ", options, " -i ", i[[1]], " -g ", g[[1]], " > ", tempfile)
if(.Platform$OS.type == "windows") shell(cmd) else system(cmd)
if(!is.null(output)) {
if(file.info(tempfile)$size > 0)
file.copy(tempfile, output)
} else {
if(file.info(tempfile)$size > 0)
results <- utils::read.table(tempfile, header=FALSE, sep="\t", quote='')
else
results <- data.frame()
}
# Delete temp files
temp.files <- c(tempfile, i[[2]], g[[2]])
if(!is.null(excl))
temp.files <- c(temp.files, excl[[2]])
if(!is.null(incl))
temp.files <- c(temp.files, incl[[2]])
deleteTempFiles(temp.files)
if(is.null(output))
return(results)
}
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