geneIdsToGeneSetCollection: Construct a GeneSetCollection object from a list of character...

In rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

Construct a GeneSetCollection object from a list of character vectors

Description

This function is essentially the reverse of GSEABase::geneIds(), i.e., it takes as input a named list of character vectors representing gene sets and returns the corresponding GeneSetCollection object.

Usage

geneIdsToGeneSetCollection(
  geneIdsList,
  geneIdType = "auto",
  collectionType = NullCollection()
)

Arguments

geneIdsList	A named list of character vectors like the ones returned by geneIds(). Names must be unique; otherwise see deduplicateGeneSets() for a number of strategies to resolve this issue.
geneIdType	By default a character vector of length 1 with the special value "auto" or an object of a subclass of GeneIdentifierType. If set to "auto", the function will try to derive the gene ID type from argument geneIdsList using guessGeneIdType. Other values, including NULL, will be ignored with a warning and geneIdType=NullIdentifier() will be used instead. The gene ID type of all GeneSet objects in the resulting GeneSetCollection will be set to this value.
collectionType	An object of class CollectionType. The collection type of all GeneSet objects in the resulting GeneSetCollection will be set to this value but can afterwards be modified for individual GeneSets if necessary.

Value

An object of class GeneSetCollection with all its GeneSet objects using the gene ID and collection types specified by the corresponding arguments. Applying function geneIds() to this object should return a list identical to the geneIdsList argument.

See Also

GeneSetCollection, geneIds, deduplicateGeneSets, guessGeneIdType, GeneSet

rcastelo/GSVA documentation built on Dec. 17, 2024, 4:51 p.m.