177 improve annotation mapping through readgmt #206
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…sGeneIdType() and geneIdsToGeneSetCollection(); update function readGMT() to make use of these new features
…dsToGeneSetCollection() and readGMT()
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This PR finally closes #177
Gene ID type can be set and retrieved for all expression data types and containers and gene sets represented as lists of character vectors using the method
gsvaAnnotation()A new function
guessGeneIdType()can be used to automatically derive the gene ID type of a list of gene sets.A new function
geneIdsToGeneSetCollection()can be used to construct aGeneSetCollectionobject from a list of character vectors.Function
readGMT()makes use of these new features and can automatically guess the gene ID type of a GMT file from MSigDb and add this metadata to the imported gene sets, regardless of their format (GeneSetCollectionor list).The metadata is used to perform gene ID mapping for gene sets with arbitrary representations of expression data and gene sets, provided that an appropriate annotation database, e.g. organism annotation, is available.