transformationProducts-class: Base transformation products (TP) class

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Base transformation products (TP) class

Description

Holds information for all TPs for a set of parents.

Usage

parents(TPs)

products(TPs)

## S4 method for signature 'transformationProducts'
parents(TPs)

## S4 method for signature 'transformationProducts'
products(TPs)

## S4 method for signature 'transformationProducts'
length(x)

## S4 method for signature 'transformationProducts'
names(x)

## S4 method for signature 'transformationProducts'
show(object)

## S4 method for signature 'transformationProducts,ANY,missing,missing'
x[i, j, ..., drop = TRUE]

## S4 method for signature 'transformationProducts,ANY,missing'
x[[i, j]]

## S4 method for signature 'transformationProducts'
x$name

## S4 method for signature 'transformationProducts'
as.data.table(x)

## S4 method for signature 'transformationProducts'
convertToSuspects(obj, includeParents = FALSE)

## S4 method for signature 'transformationProducts'
delete(obj, i = NULL, j = NULL, ...)

## S4 method for signature 'transformationProducts'
filter(obj, properties = NULL, verbose = TRUE, negate = FALSE)

Arguments

TPs, x, obj, object	transformationProducts object to be accessed
i, j	For [/[[: A numeric or character value which is used to select parents by their index or name, respectively (for the order/names see names()). For [: Can also be logical to perform logical selection (similar to regular vectors). If missing all parents are selected. For [[: should be a scalar value. For delete: The data to remove from. i are the parents as numeric index, logical or character, j the transformation products as numeric index (row) or name of the TP. If either is NULL then data for all is removed. j may also be a function: it will be called for each parent, with the TP info table (a data.table), the parent name and any other arguments passed as ... to delete. The return value of this function specifies the TP indices (rows) (specified as an integer or logical vector) or names to be removed.
...	For delete: passed to the function specified as j. Otherwise ignored.
drop	ignored.
name	The parent name (partially matched).
includeParents	If TRUE then parents are also included in the returned suspect list.
properties	A named list with properties to be filtered. Each item in the list should be named with the name of the property, and should be a vector with allowed values. To obtain the possible properties, run e.g. names(TPs)[[1]]. Example: properties=list(likelihood=c("LIKELY","PROBABLE")). Set to NULL to ignore.
verbose	If set to FALSE then no text output is shown.
negate	If TRUE then filters are performed in opposite manner.

Details

This class holds all generated data for transformation products for a set of parents. The class is virtual and derived objects are created by TP generators.

The TP data in objects from this class include a retDir column. These are numeric values that hint what the the chromatographic retention order of a TP might be compared to its parent: a value of ‘⁠-1⁠’ means it will elute earlier, ‘⁠1⁠’ it will elute later and ‘⁠0⁠’ that there is no significant difference or the direction is unknown. These values are based on a typical reversed phase separation. When structural information is available (e.g. when generateTPsBioTransformer or generateTPsLibrary was used to generate the data), the retDir values are based on calculated log P values of the parent and its TPs.

Value

delete returns the object for which the specified data was removed.

filter returns a filtered transformationProducts object.

Methods (by generic)

• parents(transformationProducts): Accessor method for the parents slot of a transformationProducts class.

• products(transformationProducts): Accessor method for the products slot.

• length(transformationProducts): Obtain total number of transformation products.

• names(transformationProducts): Obtain the names of all parents in this object.

• show(transformationProducts): Show summary information for this object.

• x[i: Subset on parents.

• x[[i: Extracts a table with TPs for a parent.

• $: Extracts a table with TPs for a parent.

• as.data.table(transformationProducts): Returns all TP data in a table.

• convertToSuspects(transformationProducts): Converts this object to a suspect list that can be used as input for screenSuspects.

• delete(transformationProducts): Completely deletes specified transformation product data.

• filter(transformationProducts): Performs rule-based filtering. Useful to simplify and clean-up the data.

Slots

parents

A data.table with metadata for all parents that have TPs in this object. Use the parents method for access.

products

A list with data.table entries with TP information for each parent. Use the products method for access.

S4 class hierarchy

• workflowStep

  • transformationProducts

    • transformationProductsStructure

      • transformationProductsStructureConsensus

      • transformationProductsCTS

      • transformationProductsBT

      • transformationProductsLibrary

    • transformationProductsFormula

      • transformationProductsLibraryFormula

    • transformationProductsLogic

See Also

The derived transformationProductsStructure class for more methods and generateTPs

rickhelmus/patRoon documentation built on April 25, 2024, 8:15 a.m.