TRAMPknowns: TRAMPknowns Objects

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

Description

These functions create and interact with TRAMPknowns objects (collections of known TRFLP patterns). Knowns contrast with “samples” (see TRAMPsamples) in that knowns contain identified profiles, while samples contain unidentified profiles. Knows must have at most one peak per enzyme/primer combination (see Details).

Usage

TRAMPknowns(data, info, cluster.pars=list(), file.pat=NULL,
            warn.factors=TRUE, ...)


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

Arguments

data	data.frame containing peak information.
info	data.frame, describing individual samples (see Details for definitions of both data.frames).
cluster.pars	Parameters used when clustering the knowns database. See Details.
file.pat	Optional partial filename in which to store knowns database after modification. Files <file.pat>_info.csv and <file.pat>_data.csv will be created.
warn.factors	Logical: Should a warning be given if any columns in info or data are converted into factors?
object	A TRAMPknowns object.
include.info	Logical: Should the output be augmented with the contents of the info component of the TRAMPknowns object?
...	TRAMPknowns: Additional objects to incorportate into a TRAMPknowns 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 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).

Value

TRAMPknowns	A new TRAMPknowns object: a list with components info, data (the provided data.frames, with clustering information added to info), cluster.pars and file.pat, plus any extra objects passed as ....
labels.TRAMPknowns	A sorted vector of the unique samples present in x (from info$knowns.pk).
summary.TRAMPknowns	A data.frame, with the size of the peak (if present) for each enzyme/primer combination, with each known (indicated by knowns.pk) as rows and each combination (in the format <primer>_<enzyme>) as columns.

Note

Across a TRAMPknowns object, primer and enzyme names must be exactly the same (including case and whitespace) to be considered the same. For example "ITS4", "Its4", "ITS 4" and "ITS4 " would be considered to be four different primers.

Factors will not merge correctly (with combine.TRAMPknowns or add.known). TRAMPknowns 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

TRAMPsamples, which constructs an analagous object to hold “samples” data.

plot.TRAMPknowns, which creates a graphical representation of the knowns data.

TRAMP, for matching unknown TRFLP patterns to TRAMPknowns objects.

group.knowns, which groups similar knowns (generally called automatically).

add.known and combine.TRAMPknowns, which provide tools for adding knowns from a sample data set and merging knowns databases.

Examples

## This example builds a TRAMPknowns object from completely artificial
## data:

## The info data.frame:
knowns.info <-
  data.frame(knowns.pk=1:8,
             species=rep(paste("Species", letters[1:5]), length=8))
knowns.info

## The data data.frame:
knowns.data <- expand.grid(knowns.fk=1:8,
                           primer=c("ITS1F", "ITS4"),
                           enzyme=c("BsuRI", "HpyCH4IV"))
knowns.data$size <- runif(nrow(knowns.data), min=40, max=800)

## Construct the TRAMPknowns object:
demo.knowns <- TRAMPknowns(knowns.data, knowns.info, warn.factors=FALSE)

## A plot of the pretend knowns:
plot(demo.knowns, cex=1, group.clusters=TRUE)

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