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#' call_tile_reg
#'
#' For a HiDRA dataset on a given chromosome, this function calls tiled regions (the regions covered by at least one read).
#' @param data A data.frame for a HiDRA dataset for one chromosome. The data.frame must contain four columns: 'start', 'end', 'PLASMID', 'RNA', and is sorted by 'start'.
#' @keywords sharpr2 HiDRA
#' @return tile_reg: A list containing the row ids in the data for each tiled region.
#' @return size the: number of reads in each tiled region.
#' @return num_r: the total number of tiled regions.
#' @export
#' @examples
#' # call_tile_reg(data)
call_tile_reg <- function(data)
{
# data <- data[order(data$start),]
reg_set <- vector("list", nrow(data))
n_s <- 0
nr <- nrow(data)
if(nr==0)
{
stop("No reads pass the quality control.")
}else{
if(nr==1)
{
n_s <- n_s + 1
reg_set[[n_s]] <- 1
}else{
pos <- data[1,'start']
i <- 1
while(i <= nr)
{
temp_set <- i
j <- i + 1
bd <- data[i,'end']
while((j<=nr)&(bd>=data[j,'start']))
{
temp_set <- c(temp_set, j)
bd <- max(bd, data[j,'end'])
j <- j + 1
}
n_s <- n_s + 1
reg_set[[n_s]] <- temp_set
i <- j
}
}
}
size <- unlist(lapply(reg_set, function(x) length(x)))[1:n_s]
return(invisible(list(tile_reg=reg_set[1:n_s], size=size, num_r = n_s)))
}
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