Retrieves information from the BioMart database
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
getBMlist(attributes, filters = "", values = "", mart, list.names = NULL, na.value = NA, verbose = FALSE, giveWarning = TRUE)
attributes |
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 |
Steffen Durinck
if(interactive()){
mart <- useMart("ensembl")
datasets <- listDatasets(mart)
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.