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.
TRAMPsamples(data, info=NULL, warn.factors=TRUE, ...)# S3 method for TRAMPsamples
labels(object, ...)
# S3 method for TRAMPsamples
summary(object, include.info=FALSE, ...)
data.frame containing peak information.
(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.
Logical: Should a warning be given if any columns
in info
or data
are converted into factors?
A TRAMPsamples
object.
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.
A new TRAMPsamples
object, as described
above.
A sorted vector of the unique samples
present in x
(from info$sample.pk
).
A data.frame, with the number of peaks
per enzyme/primer combination, with each sample (indicated by
sample.pk
) as rows and each combination (in the format
<primer>_<enzyme>
) as columns.
The object has at least two components, which relate to each other (in
the sense of a relational database). info
holds information
about the individual samples, and data
holds information about
individual peaks (many of which belong to a single sample).
Column definitions:
info
:
sample.pk
Unique positive integer, used to identify individual samples (i.e. a “primary key”).
species
Character, giving species name if samples
were collected from an identified species. If this column is
missing, it will be initialised as NA
.
data
:
sample.fk
Positive integer, indicating which sample
the peak belongs to (by matching against info$sample.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.
height
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
.
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.