get_bm: Get a table based on filters and attributes.

In c5sire/biomart2: Connects to biomart version 0.8

Description

The main difference to the biomaRt library is here that the filters are given as pairs of variable name and value separated by equal sign. Several filters can be given as a vector of such pairs. For a 'multiselection' filter multiple values can be given as a comma seperated list (see examples.)

Usage

get_bm(mart, dataset, filters = NULL, attributes, limit = NULL)

Arguments

mart	mart object
dataset	a dataset
filters	a vector variable=value pairs.
attributes	vector of attributes
limit	a number to limit the amount of returned records

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.