list_marts: List marts

In c5sire/biomart2: Connects to biomart version 0.8

Description

Valid mart names are those listed in the 'config' column of the resulting dataframe 'marts' in the response list.

Usage

list_marts(host, path = "martservice", port = 8080)

Arguments

host	The url without the http://
path	the path on the server; only if other than default 'martservice'
port	the port on the server

Value

a list object containing the parameters and the result as a dataframe in $mart

Examples

library(biomart2)

#Uncomment the following to run locally

host <- "germplasmdb.cip.cgiar.org"

if(interactive()){
  marts <- list_marts(host)
  mart  <- marts$mart$config[[4]] #dspotatov01_config
  dataset<-list_datasets(marts, mart)
  
  x=get_bm(marts, dataset$name[1], , c("acipnumber","cultvrname","female","male"),20)
  x=get_bm(marts, dataset$name[1],"fbiostat=500 Advanced or Improved cultivar", 
           c("acipnumber","cultvrname","female","male"),20)
  x=get_bm(marts, dataset$name[1],c("fbiostat=500 Advanced or Improved cultivar","fcountry=ARG,AUS"), 
           c("acipnumber","cultvrname","female","male"),20)
  x=get_bm(marts, dataset$name[1],c("fbiostat=500 Advanced or Improved cultivar","fcountry=ARG,PER"), 
           c("acipnumber","cultvrname","female","male","country"),200)
  
}

c5sire/biomart2 documentation built on May 13, 2019, 9:57 a.m.