Get/set the gene set collection url function for a geneset collection

Reference collectionMetadata() for more info.

geneSetCollectionURLfunction(x, i, ...)

geneSetCollectionURLfunction(x, i) <- value

# S4 method for class 'GeneSetDb'
geneSetCollectionURLfunction(x, i, ...)

# S4 method for class 'GeneSetDb'
geneSetCollectionURLfunction(x, i) <- value

# S4 method for class 'SparrowResult'
geneSetCollectionURLfunction(x, i, ...)

Arguments

x

The GeneSetDb

i

The collection to get the url function from

...

pass through arguments (not used)

value

the function to set as the geneset url function for the given collection i. This can be an actual function object, or the (string) name of the function to pull out of "the ether" ("pkgname::functionname" can work, too). The latter is preferred as it results in smaller serialized GeneSetDb objects.

Value

the function that maps collection,name combinations to an informational URL.

Methods (by class)

• geneSetCollectionURLfunction(GeneSetDb): returns the gene set collection url function from a GeneSetDb

• geneSetCollectionURLfunction(GeneSetDb) <- value: sets the gene set collection url function for a GeneSetDb : Collection combination.

• geneSetCollectionURLfunction(SparrowResult): return the url function from a SparrowResult object.

Examples

gdb <- exampleGeneSetDb()
geneSetCollectionURLfunction(gdb, "c2", "BIOCARTA_AGPCR_PATHWAY")
#> function (collection, name, ...) 
#> {
#>     url <- "http://www.broadinstitute.org/gsea/msigdb/cards/%s.html"
#>     sprintf(url, name)
#> }
#> <bytecode: 0x557db1025d08>
#> <environment: namespace:sparrow>