getBM {biomaRt} | R Documentation |
This function retrieves information from the BioMart database
getBM(attributes, filters, values, mart, curl = NULL, output = "data.frame", list.names = NULL, na.value = NA)
attributes |
Attributes you want to retrieve. A possible list of attributes can be retrieved using the function listAttributes. |
filters |
Filters 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. list of affy IDs |
mart |
object of class Mart, containing connections to the BioMart databases. You can creat such an object using the function useMart and update the mart object by selecting a dataset using the function useDataset. |
curl |
An optional 'CURLHandle' object, that can be used to speed up getBM when used in a loop. |
output |
Determines the output of getBM which can be either a data.frame (default) or a list. |
list.names |
In case a list was selected as output the different elements in the list can be given user defined names with this argument |
na.value |
In case a list was selected as output, the value of na.value will used when missing elements are present in the output |
Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck
if(interactive()){ mart <- useMart("ensembl") datasets <- listDatasets(mart) mart<-useDataset("hsapiens_gene_ensembl",mart) getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at"), mart=mart) }