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 may belong to a single sample).
Column definitions:
info
:
knowns.pk
:Unique positive integer, used to identify
individual knowns (i.e. a “primary key”).
species
:Character, giving species name.
data
:
knowns.fk
:Positive integer, indicating which sample
the peak belongs to (by matching against info$knowns.pk
)
(i.e. a “foreign key”).
primer
:Character, giving the name of the primer
used.
enzyme
:Character, giving the name of the
restriction digest enzyme used.
size
:Numeric, giving size (in base pairs) of the
peak.
In addition, TRAMPknowns
will create additional columns holding
clustering information (see group.knowns
). Additional
columns are allowed (and retained, but ignored) in both data.frames.
Additional objects are allowed as part of the TRAMPknowns
object, but these will not be written by
write.TRAMPknowns
; any extra objects passed (via
...
) will be included in the final TRAMPknowns
object.
The cluster.pars
argument controls how knowns will be clustered
(this will happen automatically as needed). Elements of the list
cluster.pars
may be any of the three arguments to
group.knowns
, and will be used as defaults in
subsequent calls to group.knowns
. If not provided, default
values are: dist.method="maximum"
,
hclust.method="complete"
, cut.height=2.5
(if only some
elements of cluster.pars
are provided, the remaining elements
default to the values above). To change values of clustering
parameters in an existing TRAMPknowns
object, use
group.knowns
.
A known contains at most one peak per enzyme/primer combination.
Where a species is known to have multiple TRFLP profiles, these should
be treated as separate knowns with different, unique, knowns.pk
values, but with identical species
values. A sample containing
either pattern will then be recorded as having that species present
(see group.knowns
).