TRAMPsamples             package:TRAMPR             R Documentation

_T_R_A_M_P_s_a_m_p_l_e_s _O_b_j_e_c_t_s

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

     These functions create and interact with 'TRAMPsamples' objects
     (collections of TRFLP patterns).  Samples contrast with "knowns"
     (see 'TRAMPknowns') in that samples contain primarily unidentified
     profiles.  In contrast with knowns, samples may have many peaks
     per enzyme/primer combination.

_U_s_a_g_e:

     TRAMPsamples(data, info=NULL, warn.factors=TRUE, ...)

     ## S3 method for class 'TRAMPsamples':
     labels(object, ...)
     ## S3 method for class 'TRAMPsamples':
     summary(object, include.info=FALSE, ...)

_A_r_g_u_m_e_n_t_s:

    data: data.frame containing peak information.

    info: (Optional) data.frame, describing individual samples (see
          Details for definitions of both data.frames).  If this is
          omitted, a basic data.frame will be generated.

warn.factors: Logical: Should a warning be given if any columns in
          'info' or 'data' are converted into factors?

  object: A 'TRAMPsamples' object.

include.info: Logical: Should the output be augmented with the contents
          of the 'info' component of the 'TRAMPsamples' object?

     ...: 'TRAMPsamples': Additional objects to incorportate into a
          'TRAMPsamples' object.  Other methods: Further arguments
          passed to or from other methods.

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

     The object has at least two components, which relate to each other
     (in the sense of a relational database). 'info' holds information
     about the individual samples, and 'data' holds information about
     individual peaks (many of which belong to a single sample).

     Column definitions:

        *  'info':

        '_s_a_m_p_l_e._p_k' Unique positive integer, used to identify
             individual samples (i.e. a "primary key").

        '_s_p_e_c_i_e_s' Character, giving species name if samples were
             collected from an identified species.  If this column is
             missing, it will be initialised as 'NA'.

        *  'data':

        '_s_a_m_p_l_e._f_k' Positive integer, indicating which sample the peak
             belongs to (by matching against 'info$sample.pk') (i.e. a
             "foreign key").

        '_p_r_i_m_e_r': Character, giving the name of the primer used.

        '_e_n_z_y_m_e': Character, giving the name of the restriction digest
             enzyme used.

        '_s_i_z_e' Numeric, giving size (in base pairs) of the peak.

        '_h_e_i_g_h_t' Numeric, giving the height (arbitrary units) of the
             peak.

     Additional columns are allowed (and ignored) in both data.frames,
     and will be retained.  This allows notes on data quality and
     treatments to be easily included.  Additional objects are allowed
     as part of the 'TRAMPsamples' object; any extra objects passed
     (via '...') will be included in the final 'TRAMPsamples' object.

     If 'info' is omitted, then a basic data.frame will be generated,
     containing just the unique values of 'sample.fk', and 'NA' for
     'species'.

_V_a_l_u_e:

TRAMPsamples: A new 'TRAMPsamples' object, as described above.

labels.TRAMPsamples: A sorted vector of the unique samples present in
          'x' (from 'info$sample.pk').

summary.TRAMPsamples: A data.frame, with the number of peaks per
          enzyme/primer combination, with each sample (indicated by
          'sample.pk') as rows and each combination (in the format
          '<primer>_<enzyme>') as columns.

_N_o_t_e:

     Across a 'TRAMPsamples' object, primer and enzyme names must be
     _exactly_ the same (including case and whitespace) to be
     considered the same.  For example '"ITS4"', '"Its4"', '"ITS4 "'
     and '"ITS 4"' would be considered to be four different primers.

     Factors will not merge correctly (with 'combine.TRAMPsamples'). 
     'TRAMPsamples' will attempt to catch factor columns and convert
     them into characters for the 'info' and 'data' data.frames.  Other
     objects (passed as part of '...') will not be altered.

_S_e_e _A_l_s_o:

     'plot.TRAMPsamples' and 'summary.TRAMPsamples', for plotting and
     summarising 'TRAMPsamples' objects.

     'TRAMPknowns', which constructs an analagous object to hold
     "knowns" data.

     'TRAMP', for analysing 'TRAMPsamples' objects.

     'load.abi', which creates a 'TRAMPsamples' object from Gene Mapper
     (Applied Biosystems) output.

