CORE (version 1.2)

makepairs:

Usage

makepairs(events)

Arguments

events

Value

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (events) 
{
    if ("chrom" %in% dimnames(events)[[2]]) {
        events <- events[order(events[, "chrom"]), , drop = F]
        chromstarts <- tapply(X = events[, "start"], INDEX = events[, 
            "chrom"], FUN = min)
        chromends <- tapply(X = events[, "end"], INDEX = events[, 
            "chrom"], FUN = max)
    }
    else {
        chromstarts <- min(events[, "start"])
        chromends <- max(events[, "end"])
    }
    ustarts <- sort(unique(events[, "start"]))
    uends <- sort(unique(events[, "end"]))
    z <- cbind(c(chromstarts, ustarts), c(rep(1, length(chromstarts)), 
        rep(0, length(ustarts))), c(rep(0, length(chromstarts)), 
        1:length(ustarts)))
    z <- z[order(z[, 1]), ]
    sch <- cumsum(z[, 2])[z[, 3] != 0][order(z[z[, 3] != 0, 3])]
    z <- cbind(c(chromstarts, uends), c(rep(1, length(chromstarts)), 
        rep(0, length(uends))), c(rep(0, length(chromstarts)), 
        1:length(uends)))
    z <- z[order(z[, 1]), ]
    ech <- cumsum(z[, 2])[z[, 3] != 0][order(z[z[, 3] != 0, 3])]
    sfirst <- match(1:length(chromstarts), sch)[ech]
    z <- cbind(c(ustarts, uends), c(rep(1, length(ustarts)), 
        rep(0, length(uends))))
    z <- z[order(z[, 1]), ]
    slast <- cumsum(z[, 2])[z[, 2] == 0]
    z <- cbind(rep(1:length(uends), times = (slast - sfirst + 
        1)), rep(0, sum(slast - sfirst + 1)))
    z[match(1:length(uends), z[, 1]), 2] <- match(1:length(uends), 
        z[, 1])
    mypairs <- matrix(ncol = 3, dimnames = list(NULL, c("start", 
        "end", "id")), data = c(ustarts[(1:nrow(z)) - cummax(z[, 
        2]) + sfirst[z[, 1]]], uends[z[, 1]], 1:length(uends[z[, 
        1]])))
    return(mypairs)
  }