MgsaSets-class: Sets of items and their annotations

Description Details Slots See Also Examples


This class describes sets, items and their annotations.


Internally, the method mgsa indexes all elements of the sets before fitting the model. In case mgsa must be run on several observations with the same gene sets, computations can be speeded up by performing this indexing once for all. This can be achieved by building a MgsaSets. In order to ensure consistency of the indexing, no replace method for any slot is provided. Accessors are available.

The data frames setAnnotations and itemAnnotations allow to store annotations. No constraint is imposed on the number and names of their columns.



A list whose elements are vector of item indices.


The mapping of item names to index.


How many items?


Annotations of the sets. The rownames are set names.


Annotations of the items. The rownames are item names.

See Also

MgsaGoSets, readGAF, mgsa


new("MgsaSets", sets=list(set1=c("a", "b"), set2=c("b", "c")))

mgsa documentation built on May 20, 2017, 9:39 p.m.
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