R: Retrieves information from the BioMart database
getBMlist
R Documentation
Retrieves information from the BioMart database
Description
This function is the main biomaRt query function. Given a set of filters and corresponding values, it retrieves the user specified attributes from the BioMart database one is connected to
Attributes you want to retrieve. A possible list of attributes can be retrieved using the function listAttributes.
filters
Filters (one or more) that should be used in the query. A possible list of filters can be retrieved using the function listFilters.
values
Values of the filter, e.g. vector of affy IDs. If multiple filters are specified then the argument should be a list of vectors of which the position of each vector corresponds to the position of the filters in the filters argument.
mart
object of class Mart, created with the useMart function.
list.names
names for objects in list
na.value
value to give when result is empty
verbose
When using biomaRt in webservice mode and setting verbose to TRUE, the XML query to the webservice will be printed.
giveWarning
Gives a warning about best practices of biomaRt and recommends using getBM instead of getBMlist
Author(s)
Steffen Durinck
Examples
if(interactive()){
mart <- useMart("ensembl")
datasets <- listDatasets(mart)
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(biomaRt)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biomaRt/getBMlist.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getBMlist
> ### Title: Retrieves information from the BioMart database
> ### Aliases: getBMlist
> ### Keywords: methods
>
> ### ** Examples
>
> #if(interactive()){
> mart <- useMart("ensembl")
> datasets <- listDatasets(mart)
>
> #}
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.