R Graphical Manual

Last data update: 2014.03.03

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dbImport (Package: plethy) :

The main purpose of this function is to add data originally retrieved from the retrieveData method into a new or existing BuxcoDB database. This will most frequently be useful in the context of a merging procedure, however it also can facilitate data sharing and/or communication between seperate DBMS systems.

● Data Source: BioConductor
● Keywords: utilities
● Alias: dbImport
● 0 images

Buxco file Parsers (Package: plethy) :

A typical Buxco respirometry experiment involves collecting repeated measures on both acclimation and experimental data related to metabolism and respiration. The parse.buxco function creates a local database representation of a given file to facilitate fast retrieval and ultimately analysis. The user should only use parse.buxco with parse.buxco.basic mainly used for testing purposes.

● Data Source: BioConductor
● Keywords: utilities
● Alias: parse.buxco, parse.buxco.basic
● 0 images

plethy-package (Package: plethy) :

This package provides the infrastructure and tools to import, query and perform basic analysis of whole body plethysmography and metabolism data. Currently support is limited to data derived from Buxco respirometry instruments as exported by their FinePointe software.

● Data Source: BioConductor
● Keywords: package
● Alias: buxco.sample.data.path, plethy, plethy-package, sample.db.path
● 0 images

Utility functions (Package: plethy) :

After creation of a database, often additional data needs to be added or modified. These functions assist with the common tasks that occur when working with Buxco whole body plethysmography data such as adding labels based on the sample IDs in the case of add.labels.by.sample or modifying labels that have previously been added in the case of adjust.labels. The get.err.breaks function produces a summary of the samples and timepoints that have the specified value for the 'Break_type_label' column (such as 'ERR' or 'UNK') and whether they are close to the expected value for either and experimental or acclimation run. This can occur if there was only an experimental run for some samples or if other anomalies occured. The user can then inspect these new labels wihtin the data.frame, modify them manually if necessary and use the data.frame as input to the adjust.labels function which replaces the original labels and moves the original labels to another column for future reference.

● Data Source: BioConductor
● Keywords: Utilities
● Alias: add.labels.by.sample, adjust.labels, get.err.breaks, proc.sanity
● 0 images

BuxcoDB-class (Package: plethy) : Class code{"BuxcoDB"

This is the main class of the plethy package. Each object of this class simply holds the name of the database as well as the name(s) of any additional tables added through addAnnotation.

● Data Source: BioConductor
● Keywords: classes
● Alias: BuxcoDB, BuxcoDB-class, addAnnotation, addAnnotation,BuxcoDB-method, annoCols, annoCols,BuxcoDB-method, annoLevels, annoLevels,BuxcoDB-method, annoTable, annoTable,BuxcoDB-method, dbName, dbName,BuxcoDB-method, makeBuxcoDB, mvtsplot, mvtsplot,BuxcoDB-method, retrieveData, retrieveData,BuxcoDB-method, retrieveMatrix, retrieveMatrix,BuxcoDB-method, samples, samples,BuxcoDB-method, summaryMeasures, summaryMeasures,BuxcoDB-method, tables, tables,BuxcoDB-method, tsplot, tsplot,BuxcoDB-method, variables, variables,BuxcoDB-method
● 0 images

Additional annotation queries (Package: plethy) :

These functions take BuxcoDB objects as input and return an SQL query (in the SQLite dialect) which results in the creation of a table containing additional annotation that is not parsed from the Buxco CSV file. These annotations are meant to be categorical labels such as whether a datapoint was part of an acclimation or experimental run which may not necessarily be encoded directly in the Buxco CSV file. A user can also specify functions in this form to add custom annotations to the database. Typically the end user does not need to call these functions directly, instead they are supplied to the code argument of the addAnnotation method. This method then calls the function internally in the process of generating the annotation table.

● Data Source: BioConductor
● Keywords: utilities
● Alias: break.type.query, day.infer.query
● 0 images