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Initiate sets workflows

Source: R/generics.R, R/main.R, R/features-set.R, and 1 more
makeSet.Rd

Initiate sets workflows from specified feature data.

Usage

makeSet(obj, ...)

# S4 method for class 'features'
makeSet(obj, ..., adducts, labels = NULL)

# S4 method for class 'featuresSet'
makeSet(obj, ...)

# S4 method for class 'featureGroups'
makeSet(
  obj,
  ...,
  groupAlgo,
  groupArgs = NULL,
  verbose = TRUE,
  adducts = NULL,
  labels = NULL
)

# S4 method for class 'featureGroupsSet'
makeSet(obj, ...)

Arguments

obj, ...

features or featureGroups objects that should be used for the sets workflow.

adducts

The adduct assignments to each set. Should either be a list with adduct objects or a character vector (e.g. "[M+H]+"). The order should follow that of the objects given to the obj and ... arguments.

For the featureGroups method: if NULL then adduct annotations are used.

labels

The labels, or set names, for each set to be created. The order should follow that of the objects given to the obj and ... arguments. If NULL, then labels are automatically generated from the polarity of the specified adducts argument (e.g. "positive", "negative").

groupAlgo

groupAlgo The name of the feature grouping algorithm. See the algorithm argument of groupFeatures for details.

groupArgs

A list with arguments directly passed to groupFeatures (can be named). Example: groupArgs=list(maxAlignMZ=0.002).

verbose

If set to FALSE then no text output is shown.

Value

Either a featuresSet object (features method) or featureGroupsSet object (featureGroups method).

Details

The makeSet method function is used to initiate a sets workflow. The features from input objects are combined and then neutralized by replacing their m/z values by neutral monoisotopic masses. After neutralization features measured with e.g. different ionization polarities can be grouped since their neutral mass will be the same.

The analysis information for this object is updated with all analyses, and a set column is added to designate the set of each analysis. Note that currently, all analyses names must be unique across different sets.

makeSet supports two types of input:

  1. features objects: makeSet combines the input objects into a featuresSet object, which is then grouped in the 'usual way' with groupFeatures.

  2. featureGroups objects: In this case the features from the input objects are first neutralized and feature groups between sets are then combined with groupFeatures.

The advantage of the featureGroups method is that it preserves any adduct annotations already present (e.g. as set by selectIons or adducts<-). Furthermore, this approach allows more advanced workflows where the input featureGroups are first pre-treated with e.g. filter before the sets object is made. On the other hand, the features method is easier, as it doesn't require intermediate feature grouping steps and is often sufficient since adduct annotations can be made afterwards with selectIons/adducts<- and most filter operations do not need to be done per individual set.

The adduct information used for feature neutralization is specified through the adducts argument. Alternatively, when the featureGroups method of makeSet is used, then the adduct annotations already present in the input objects can also by used by setting adducts=NULL. The adduct information is also used to add adduct annotations to the output of makeSet.

Note

Initiating a sets workflow recursively, i.e. with featuresSet or featureGroupsSet objects as input, is currently not supported.