addMetaFeaturesLinkouts {OmicNavigator}

Add linkouts to external resources in the metaFeatures table

Description

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

Usage

addMetaFeaturesLinkouts(study, metaFeaturesLinkouts, reset = FALSE)

Arguments

study

An OmicNavigator study created with createStudy

metaFeaturesLinkouts

The URL patterns that describe linkouts to external resources (see Details below). The input object is a nested named list. The names of the list correspond to the model names. Each element of the list is a named list of character vectors. The names of this nested list must correspond to the column names of the matching metaFeatures table (addMetaFeatures). To share linkouts across multiple models, use the modelID "default".

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 that column for each row. As an example, if your metaFeatures table included a column named "ensembl" that contained the Ensembl Gene ID for each feature, you could create a linkout to Ensembl using the following pattern:

ensembl = "https://ensembl.org/Homo_sapiens/Gene/Summary?g="

As another example, if you had a column named "entrez" that contained the Entrez Gene ID for each feature, you could create a linkout to Entrez using the following pattern:

entrez = "https://www.ncbi.nlm.nih.gov/gene/"

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

Value

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

See Also

addMetaFeatures

Examples

  study <- createStudy("example")
  metaFeaturesLinkouts <- list(
    default = list(
      ensembl = c("https://ensembl.org/Homo_sapiens/Gene/Summary?g=",
                  "https://www.genome.ucsc.edu/cgi-bin/hgGene?hgg_gene="),
      entrez = "https://www.ncbi.nlm.nih.gov/gene/"
    )
  )
  study <- addMetaFeaturesLinkouts(study, metaFeaturesLinkouts)