TRAMPR-package: The TRAMPR Package (TRFLP Analysis and Matching Package for...

Description Details Citation Note Author(s) References

Description

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).

Details

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.

Citation

Please see citation("TRAMPR") for the citation of TRAMPR.

Note

TRAMPR is designed specifically for “database TRFLP” (identifying species based on a database of known TRFLP profiles: see Dicke et al. 2002. It is not designed for direct community analysis of TRFLP profiles as in peak-profile TRFLP.

Author(s)

Rich FitzJohn and Ian Dickie, Landcare Research

References

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].


richfitz/TRAMPR documentation built on May 25, 2017, 2:07 a.m.