I'm learning Bioconductor but can't seem to understand how Biostrings::coverage() works.

During the class I was taught that coverage "counts, for each integer, how many ranges overlap the integer.".

Another definition I found in the documentation of the IRanges package (coverage methods) is "For each position in the space underlying a set of ranges, counts the number of ranges that cover it."

So if I have the following IRanges
> ir <- IRanges(start = c(2,6), width = 2)

and compute the coverage
> coverage(ir)

I would expect to get back an Rle where as Values I have all the integer that a covered by the IRanges (meaning 2 3 6 7) and as Lengths I have the number of times those integer are "covered" by the ranges in the IRanges. In this example this would mean

integer-Rle of length 4 with 4 runs
  Lengths: 1 1 1 1
  Values : 2 3 6 7

Except that the returned Rle is something entirely different:

> coverage(ir)
integer-Rle of length 7 with 4 runs

  Lengths: 1 2 2 2
  Values : 0 1 0 1

> as.numeric(coverage(ir))
[1] 0 1 1 0 0 1 1

Can someone explain me why are there 0s an 1s as Values when neither of this two integer is actually part of the input IRanges? And why do they repeat? I simply can't understand how this Rle is representing the inputted IRanges...

It's like eating pizza. Take a pizza and cut it into seven pieces. Arrange the pieces in a row, and place the numbers 1 through 7 over pieces 1 through 7.

Position          1 2 3 4 5 6 7
How many pieces?  1 1 1 1 1 1 1

Now eat pieces 1, 4 and 5. Create a vector that counts the number of pieces of pizza over number 1, 2, 3, 4, 5, 6, and 7.

Position          1 2 3 4 5 6 7
How many pieces?  0 1 1 0 0 1 1

 If I've done my eating right, I've got 0, 1, 1, 0, 0, 1, and 1 pieces of pizza covering the numbers 1 through 7, respectively. I could summarize that vector as

Length: 1 2 2 2
Value:  0 1 0 1

Which is to say there was 1 position with 0 pieces of pizza, then 2 positions each with 1 piece of pizza, followed by 2 positions with 0 pieces of pizza, and finally 2 positions each with 1 piece of pizza.

Hope that helps. Time for dinner!

If you have an Rle cov then cov[i] represents the number of ranges overlapping position i. The Rle is a run-length encoding, which is equivalent to the integer vector generated by rep(runValue(cov), runLength(cov)).