Directly . . . in R? Unless you only have a tiny number of reads, I doubt you'll find any usable solution. R is absolutely not the right language for a tool implementing that type of functionality, and I doubt anyone has spent time in a serious effort to write an all-R short read mapper. That being said, there are packages (written in C++) for read mapping that expose an R interface. For example, I know that the subread aligner exposes an R interface.

If you are trying to align sequencing data with R, you are doing it wrong.

@pierre do you know where I can find examples ofa genome and its fastq read file?