getLDS: Retrieves information from two linked datasets

In grimbough/biomaRt: Interface to BioMart databases (i.e. Ensembl)

Retrieves information from two linked datasets

Description

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.

Usage

getLDS(attributes, filters = "", values = "", mart, attributesL,
filtersL = "", valuesL = "", martL, verbose = FALSE, uniqueRows = TRUE, 
bmHeader=TRUE)

Arguments

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
bmHeader	Boolean to indicate if the result retrieved from the BioMart server should include the data headers or not, defaults to TRUE. This should only be switched off if the default behavior results in errors, setting to off might still be able to retrieve your data in that case

Author(s)

Steffen Durinck

Examples

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)
}

grimbough/biomaRt documentation built on Aug. 7, 2024, 8:56 p.m.