TRAMPsamples {TRAMPR} | R Documentation |
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 class 'TRAMPsamples': labels(object, ...) ## S3 method for class 'TRAMPsamples': summary(object, include.info=FALSE, ...)
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. |
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
species
NA
.data
:
sample.fk
info$sample.pk
)
(i.e. a “foreign key”).primer
:enzyme
:size
height
Additional columns are allowed (and ignored) in both data.frames, and
will be retained. This allows notes on data quality and treatments to
be easily included. Additional objects are allowed as part of the
TRAMPsamples
object; any extra objects passed (via
...
) will be included in the final TRAMPsamples
object.
If info
is omitted, then a basic data.frame will be generated,
containing just the unique values of sample.fk
, and
NA
for species
.
TRAMPsamples |
A new TRAMPsamples object, as described
above. |
labels.TRAMPsamples |
A sorted vector of the unique samples
present in x (from info$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. |
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.
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.