Hi, 

I found a presentation about the GenomicFeatures and its basic function.

In there, I found a function called plotCoverage. I am interested in what it does. Can someone explain it to me?

 plotCoverage <-function(x, chrom, start=1, end=length(x[[chrom]]), col="blue",
    xlab="Index", ylab="Coverage", main=chrom)
   {
    xWindow <- as.vector(window(x[[chrom]], start, end))
      x <- start:end
      xlim <- c(start, end)
      ylim <- c(0, max(xWindow))
     plot(x = start, y = 0, xlim = xlim, ylim = ylim,
     xlab = xlab, ylab = ylab, main = main, type = "n")
      polygon(c(start, x, end), c(0, xWindow, 0), col = col)
       }

The problem is with the term coverage. What does coverage mean here? Is it about how many times a base is
covered by reads or is it about the fragments or ranges mapped along the chromosome?

Source:
http://master.bioconductor.org/help/course-materials/2010/EMBL2010/GenomicRanges.pdf

We typically define coverage as the number of features overlapping a genomic position.

That function is just going to plot a vector (from a list "x", the element corresponding to "chrom") of Y values from the start index to end index (the X values). It does not really matter what the Y values are. I think Deepayan wrote it for our ChIP-seq course. At this point, I would recommend using ggbio, Gviz or epivizr to view coverage data.