TRAMPsamples: TRAMPsamples Objects

In richfitz/TRAMPR: 'TRFLP' Analysis and Matching Package for R

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.

See Also

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.

richfitz/TRAMPR documentation built on Feb. 10, 2022, 3:10 p.m.