R/getWinFromIRanges.R

In strandCheckR: Calculate strandness information of a bam file

#' @title Get the Ranges of Sliding Windows from an IRanges object
#' 
#' @description Get the Ranges of Sliding Windows from an IRanges object
#' 
#' @details
#' This finds the windows that overlap each fragment of a read and returns a 
#' range containing
#' this list of windows for each read fragment.
#' This allows the total number of read fragments within a window to be 
#' calculated simply using \link{coverage}.
#' 
#' @param x an IRanges object containing the start and end position of 
#' each read fragment
#' @param winWidth The width of each window
#' @param winStep The step size for sliding the window
#' @param readProp A read is considered to be included in a window if at least 
#' \code{readProp} of it is in the window. Specified as a proportion.
#' @param maxWin The maximum window ID
#' 
#' @return An IRanges object containing the index of the windows containing 
#' each read fragment
#' 
#'
getWinFromIRanges <- function(
    x, winWidth = 1000L, winStep = 100L, readProp = 0.5, maxWin = Inf
    ) 
{   
    readProp <- readProp[1]
    if (readProp <= 0 || readProp > 1) {
        stop("readProp must be within the range (0, 1]")
    }
    
    stopifnot(is.numeric(maxWin))
    
    # Calculate the index of the first window that overlaps a fragment
    startWin <- 
        ceiling((start(x) - winWidth + (readProp) * width(x))/winStep) + 1
    startWin[startWin < 1] <- 1
    startWin[startWin > maxWin] <- maxWin
    
    # Calculate the index of the final window that overlaps a fragment
    endWin <- floor((end(x) - 1 - (readProp) * width(x))/winStep) + 1
    endWin[endWin > maxWin] <- maxWin
    # Return the complete set of windows for each fragment
    IRanges(start = startWin, end = endWin)
}