This package contains a collection of functions to help analyse terminal restriction fragment length polymorphism (TRFLP) profiles, by matching unknown peaks to known TRFLP profiles in order to identify species.
The TRAMPR package contains a vignette, which includes a worked
example; type vignette("TRAMPRdemo") to view it. To see all
documented help topics, type library(help=TRAMPR).
Please see citation("TRAMPR") for the citation of
TRAMPR.
Start by reading the TRAMP (and perhaps
create.diffsmatrix) help pages, which explain the
matching algorithm.
Then read load.abi to learn how to load ABI format data
into the program. Alternatively, read TRAMPsamples and
read.TRAMPsamples to load already-processed data.
If you already have a collection of knowns, read
TRAMPknowns and read.TRAMPknowns to learn
how to load them. Otherwise, read build.knowns to learn
how to automatically generate a set of known profiles from your data.
Once your data are loaded, reread TRAMP to do the
analysis, then read plot.TRAMP and
summary.TRAMP to examine the analysis.
update.TRAMP may also be useful for modifying your
matches. summary.TRAMP is also useful for preparing
presence/absence matrices for analysis with other tools (e.g. the
vegan package; see the vignette indicated below).
TRAMPR works with database-like objects, and a basic understanding of relational databases and primary/foreign keys will aid in understanding some aspects of the package.
Dicke IA, FitzJohn RG 2007: Using terminal-restriction fragment length polymorphism (T-RFLP) to identify mycorrhizal fungi; a methods review. Mycorrhiza 17: 259-270.
Dickie IA, Xu B, Koide RT 2002. Vertical distribution of ectomycorrhizal hyphae in soil as shown by T-RFLP analysis. New Phytologist 156: 527-535.
FitzJohn RG, Dickie IA 2007: TRAMPR: An R package for analysis and matching of terminal-restriction fragment length polymorphism (TRFLP) profiles. Molecular Ecology Notes [doi:10.1111/j.1471-8286.2007.01744.x].