getLDS {biomaRt} | R Documentation |
This function is the main biomaRt query function that links 2 datasets and retrieves information from these linked BioMart datasets. In Ensembl this translates to homology mapping.
getLDS(attributes, filters = "", values = "", mart, attributesL, filtersL = "", valuesL = "", martL, verbose = FALSE, uniqueRows = TRUE)
attributes |
Attributes you want to retrieve of primary dataset. A possible list of attributes can be retrieved using the function listAttributes. |
filters |
Filters that should be used in the query. These filters will be applied to primary dataset. 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 created with the useMart function. |
attributesL |
Attributes of linked dataset that needs to be retrieved |
filtersL |
Filters to be applied to the linked dataset |
valuesL |
Values for the linked dataset filters |
martL |
Mart object representing linked dataset |
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 |
Logical to indicate if the BioMart web service should return unique rows only or not. Has the value of either TRUE or FALSE |
Steffen Durinck, http://www.stat.berkeley.edu/~steffen
if(interactive()){ human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", values = "TP53", mart = human, attributesL = c("chromosome_name","start_position"), martL = mouse) }