#' Clusters overlapping/nearby BED/GFF/VCF intervals.
#'
#' @param i <bed/gff/vcf>
#' @param s Force strandedness. That is, only merge features
#' that are the same strand.
#' - By default, merging is done without respect to strand.
#'
#' @param d Maximum distance between features allowed for features
#' to be merged.
#' - Def. 0. That is, overlapping & book-ended features are merged.
#' - (INTEGER)
#'
#' @param output Output filepath instead of returning output in R.
#'
bt.cluster <- function(i, s = NULL, d = NULL, output = NULL)
{
# Required Inputs
i <- establishPaths(input=i, name="i", allowRobjects=TRUE)
options <- ""
# Options
options <- createOptions(names=c("s", "d"), values=list(s, d))
# 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 cluster ", options, " -i ", i[[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]])
deleteTempFiles(temp.files)
if(is.null(output))
return(results)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.