R: TRAMPsamples Objects

TRAMPsamples {TRAMPR}

R Documentation

TRAMPsamples Objects

Description

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.

Usage

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

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

Arguments

`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.

Details

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.

Value

`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.

Note

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.