1. Download RStudio: http://www.rstudio.com/ It is user interface for R and works great on windows. It is easier to start learning R using RStudio since you can see what its going on on each step, you can visualize the plots at the moment, well, in my opinion is good for beginners.

2. Download Rsamtools. Open Rstudio and:

source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

3. Read Rsamtools documentation: http://www.bioconductor.org/packages/release/bioc/vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf

4. Try to do it yourself.

5. Come back here if you have problems or specific questions.

I don't want to be rude, but you should try to get the solution yourself. It's the only way to learn.

For other hand, if you are not familiar with R, you can get the genome coverage using another tools like samtools, bedtools... etc.