addEnrichmentsLinkouts {OmicNavigator}

Add linkouts to external resources in the enrichments table

Description

You can provide additional information on the annotation terms in your study by providing linkouts to external resources. These will be embedded directly in the enrichments table.

Usage

addEnrichmentsLinkouts(study, enrichmentsLinkouts, reset = FALSE)

Arguments

study

An OmicNavigator study created with createStudy

enrichmentsLinkouts

The URL patterns that describe linkouts to external resources (see Details below). The input object is a named list. The names of the list correspond to the annotation names. Each element of the list is a character vector of linkouts for that annotationID.

reset

Reset the data prior to adding the new data (default: FALSE). The default is to add to or modify any previously added data (if it exists). Setting reset = TRUE enables you to remove existing data you no longer want to include in the study.

Details

For each linkout, the URL pattern you provide will be concatenated with the value of the termID column. As an example, if you used the annotation database AmiGO 2 for your enrichments analysis, you can provide a linkout for each termID using the following pattern:

go = "https://amigo.geneontology.org/amigo/term/"

As another example, if you used the annotation database Reactome for your enrichments analysis, you can provide a linkout for each termID using the following pattern:

reactome = "https://reactome.org/content/detail/"

Note that you can provide more than one linkout per termID.

Value

Returns the original onStudy object passed to the argument study, but modified to include the newly added data

See Also

addAnnotations, addEnrichments

Examples

  study <- createStudy("example")
  enrichmentsLinkouts <- list(
    gobp = c("https://amigo.geneontology.org/amigo/term/",
             "https://www.ebi.ac.uk/QuickGO/term/"),
    reactome = "https://reactome.org/content/detail/"
  )
  study <- addEnrichmentsLinkouts(study, enrichmentsLinkouts)