How to read .bam file in Rsamtools R package?

Question

[M K]

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.

Answer 1

[Danielk]

Did you try the package vignette?

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

[M K]

Hi Danielk, I used the Rsamtools package and I follow the the example in the pdf and it works. But I need to use my .bam file not the one provided in the pdf file. Also, I need to read all information in this file (not a portion).