data-raw/template.R

In robertamezquita/Inkwell: Containers for Curated Cell Type Signatures

## Template for creating a new geneset
##
## This is the information that should be used for creating stored genesets
##
## Key values:
## - setName  : human readable set name, associated with a cell type
## - type     : see ?GSEABase::GeneIdentifierType for more possible values,
##              most useful are `SymbolIdentifier`, `ENSEMBLIdentifier`, and `EntrezIdentifier()`
##              an argument inside specifies the AnnotationDBI object to which it refers, such
##              as `org.Hs.eg.db` or `org.Mm.eg.db` (human and mouse, respectively)
## - organism : human readable organism name that refer to above AnnotationDBI object
## - geneIds  : the gene IDs comprising the geneset
##
## Metadata values:
## - urls : URL referring to publication or other online resource from which derived
## - contributor : person contributing the geneset (not necessarily the author)
## - pubMedIds : if available, associated publication
## - creationDate : character value of date in "YYYY-MM-DD" format
##
## Example:
##
## gs <- GeneSet(
##     setName = 'CD4 T cells', 
##     ## setIdentifier = 'a', # not used
##     type = SymbolIdentifier('org.Hs.eg.db'), 
##     organism = 'Homo sapiens', 
##     geneIds = 'IL7R',
##     urls = 'https://www.yoururl.org',
##     contributor = 'Robert A. Amezquita',
##     pubMedIds = '30496498',
##     creationDate = '2018-01-01'
##     ## collectionType = NullCollection() # manual
## )