#' Merges overlapping BED/GFF/VCF entries into a single interval.
#'
#' @param i <bed/gff/vcf>
#' @param s Force strandedness. That is, only merge features
#' that are on the same strand.
#' - By default, merging is done without respect to strand.
#'
#' @param S Force merge for one specific strand only.
#' Follow with + or - to force merge from only
#' the forward or reverse strand, respectively.
#' - 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)
#' - Note: negative values enforce the number of b.p. required for overlap.
#'
#' @param c Specify columns from the B file to map onto intervals in A.
#' Default: 5.
#' Multiple columns can be specified in a comma-delimited list.
#'
#' @param o Specify the operation that should be applied to -c.
#' Valid operations:
#' sum, min, max, absmin, absmax,
#' mean, median, mode, antimode
#' stdev, sstdev
#' collapse (i.e., print a delimited list (duplicates allowed)),
#' distinct (i.e., print a delimited list (NO duplicates allowed)),
#' distinct_sort_num (as distinct, sorted numerically, ascending),
#' distinct_sort_num_desc (as distinct, sorted numerically, desscending),
#' distinct_only (delimited list of only unique values),
#' count
#' count_distinct (i.e., a count of the unique values in the column),
#' first (i.e., just the first value in the column),
#' last (i.e., just the last value in the column),
#' Default: sum
#' Multiple operations can be specified in a comma-delimited list.
#' If there is only column, but multiple operations, all operations will be
#' applied on that column. Likewise, if there is only one operation, but
#' multiple columns, that operation will be applied to all columns.
#' Otherwise, the number of columns must match the the number of operations,
#' and will be applied in respective order.
#' E.g., "-c 5,4,6 -o sum,mean,count" will give the sum of column 5,
#' the mean of column 4, and the count of column 6.
#' The order of output columns will match the ordering given in the command.
#'
#' @param delim Specify a custom delimiter for the collapse operations.
#' - Example: -delim "|"
#' - Default: ",".
#'
#' @param prec Sets the decimal precision for output (Default: 5)
#'
#' @param bed If using BAM input, write output as BED.
#'
#' @param header Print the header from the A file prior to results.
#'
#' @param nobuf Disable buffered output. Using this option will cause each line
#' of output to be printed as it is generated, rather than saved
#' in a buffer. This will make printing large output files
#' noticeably slower, but can be useful in conjunction with
#' other software tools and scripts that need to process one
#' line of bedtools output at a time.
#'
#' @param iobuf Specify amount of memory to use for input buffer.
#' Takes an integer argument. Optional suffixes K/M/G supported.
#' Note: currently has no effect with compressed files.
#'
#' @param output Output filepath instead of returning output in R.
#'
bt.merge <- function(i, s = NULL, S = NULL, d = NULL, c = NULL, o = NULL, delim = NULL, prec = NULL, bed = NULL, header = NULL, nobuf = NULL, iobuf = NULL, output = NULL)
{
# Required Inputs
i <- establishPaths(input=i, name="i", allowRobjects=TRUE)
options <- ""
# Options
options <- createOptions(names=c("s", "S", "d", "c", "o", "delim", "prec", "bed", "header", "nobuf", "iobuf"), values=list(s, S, d, c, o, delim, prec, bed, header, nobuf, iobuf))
# 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 merge ", 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)
}
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