Shiny module for searching BEIDs

Usage

beidsServer(
  id,
  toGene = TRUE,
  multiple = FALSE,
  beOfInt = NULL,
  selectBe = TRUE,
  orgOfInt = NULL,
  selectOrg = TRUE,
  tableHeight = 150
)

beidsUI(id)

Arguments

id: an identifier for the module instance
toGene: focus on gene entities (default=TRUE): matches from other BE are converted to genes.
multiple: allow multiple selections (default=FALSE)
beOfInt: if toGene==FALSE, BE to consider (default=NULL ==> all)
selectBe: if toGene==FALSE, display an interface for selecting BE
orgOfInt: organism to consider (default=NULL ==> all)
selectOrg: display an interface for selecting organisms
tableHeight: height of the result table (default: 150)

Value

A reactive data.frame with the following columns:

beid: the BE identifier
preferred: preferred identifier for the same BE in the same scope
be: the type of biological entity
source: the source of the identifier
organism: the BE organism
entity: internal identifier of the BE
match: the matching character string

Functions

beidsUI():

Examples

if (FALSE) {
library(shiny)
library(BED)
library(DT)

ui <- fluidPage(
   beidsUI("be"),
   fluidRow(
      column(
         12,
         tags$br(),
         h3("Selected gene entities"),
         DTOutput("result")
      )
   )
)

server <- function(input, output){
   found <- beidsServer("be", toGene=TRUE, multiple=TRUE, tableHeight=250)
   output$result <- renderDT({
      req(found())
      toRet <- found()
      datatable(toRet, rownames=FALSE)
   })
}

shinyApp(ui = ui, server = server)
}