TRAMPR-package            package:TRAMPR            R Documentation

_T_h_e _T_R_A_M_P_R _P_a_c_k_a_g_e (_T_R_F_L_P _A_n_a_l_y_s_i_s _a_n_d _M_a_t_c_h_i_n_g _P_a_c_k_a_g_e _f_o_r _R)

_D_e_s_c_r_i_p_t_i_o_n:

     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)'.

_D_e_t_a_i_l_s:

     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.

_C_i_t_a_t_i_o_n:

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

_N_o_t_e:

     '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.

_A_u_t_h_o_r(_s):

     Rich FitzJohn and Ian Dickie, Landcare Research

_R_e_f_e_r_e_n_c_e_s:

     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].

