I have an `accepted_hits.bam` file which is from tophat output, and I need to use Rsamtools "R package" to do some analysis for the `.bam` file. So any one know how to read this file in R.
Did you try the package vignette?

http://www.bioconductor.org/packages/2.13/bioc/vignettes/Rsamtools/inst/doc/Rsamtools-Overview.pdf