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.
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
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(biomaRt)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/biomaRt/getLDS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getLDS
> ### Title: Retrieves information from two linked datasets
> ### Aliases: getLDS
> ### Keywords: methods
>
> ### ** 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)
HGNC.symbol Chromosome.Name Gene.Start..bp. Chromosome.Name.1
1 TP53 17 7661779 11
Gene.Start..bp..1
1 69580359
> #}
>
>
>
>
>
> dev.off()
null device
1
>