I'm having some difficulty with the GenomicRanges package.  Probably something simple that I'm just not seeing. I'm looking to work with some BAM files in R using the GenomicRanges package.  After loading the library, I query the readGAlignments function and it does not appear to exist in the environment.

I use ls("package:GenomicRanges") to see the contents of the package and have found that it is missing classes and functions related to gapped alignments (e.g. no GAlignments-class or readGAlignments() function).

I am using R version 3.2.2, Bioconductor 2.10, GenomicRanges 1.20.8. 

Thanks for any help!

Jay Duffner, Senior Scientist

Momenta Pharmaceuticals

Cambridge, MA

I found the gapped alignment-related functions in the GenomicAlignments package.  I'll write a note to the GenomicRanges package authors as some of the documentation indicates in the GenomicRanges package indicates that these functions are in the GenomicRanges package.