binner is an R package for processing DNA fingerprint data. At present, it
provides a complete workflow for AFLP analysis:
- reading ABI
- normalizing electropherograms
- identifying and sizing peaks
- viewing individual electropherograms
- dropping, adding and renaming samples
- Automated peak-binning, using the
- Generating presence-absence matrices for further analysis in R (or export for use in other programs, if you like)
You can install
binner using Hadley Wickham's
There is no vignette for the package. I have provided a reasonably complete
example in the help file for the function
readFSA. Open it from with R
?readFSA (after you've loaded binner of course).
There are two R-based alternatives you may like to consider as well:
RawGeno currently requires the use of a second program,
to read the raw fsa data.
binner is a bit slower than
reading fsa files, but implements the same sizing algorithm (local
southern). Parts of
binner may make their way into the next version of
RawGeno, and the current version of
binner has pilfered some key bits of
RawGeno (most notably the binning algorithm).
If working entirely in R is useful to you,
binner is currently preferable
binner also provides a GUI for checking and editing your bins.
Beyond that it's a matter of preference.
AFLP provides a more sophisticated workflow than
provides a very powerful system for controlling for variation between
capillaries, sequencers, sequencing runs etc. However, it seems to use a
different sizing system, making it hard to make direct comparisons between
electropherograms processed with
AFLP and those using the