getBM {biomaRt} | R Documentation |
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
getBM(attributes, filters = "", values = "", mart, curl = NULL, output = "data.frame", list.names = NULL, na.value = NA, checkFilters = TRUE, verbose = FALSE, uniqueRows = 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. |
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 |
checkFilters |
Sometimes attributes where a value needs to be specified, for example upstream_flank with value 20 for obtaining upstream sequence flank regions of length 20bp, are treated as filters in BioMarts. To enable such a query to work, one must specify the attribute as a filter and set checkFilters = FALSE for the query to work. |
verbose |
When using biomaRt in webservice mode and setting verbose to TRUE, the XML query to the webservice will be printed. Alternatively in MySQL mode the MySQL query will be printed. |
uniqueRows |
If the result of a query contains multiple identical rows, setting this argument to TRUE (default) will result in deleting the duplicated rows in the query result at the server side. |
Steffen Durinck, http://www.stat.berkeley.edu/~steffen
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) }