getBioMartData: getBioMartData

In snplist: Tools to Create Gene Sets

Description

A function leveraging the biomaRt package to retrieve gene chromosome and start and end positions from Ensembl.

Usage

    getBioMartData(genes,verbose=FALSE,...) 

Arguments

genes	A vector of gene names matching hgnc_symbol in the Ensembl database.
verbose	A Boolean indicating whether to output the funcitons progress in terms of the dimensions of the data.frame being constructed. Default is FALSE.
...	Additional arguments passed on to the internal call to biomaRt::useMart(...). If no such arguments are provided, useMart("ensembl", dataset="hsapiens_gene_ensembl") is run by default.

Value

A data.frame object with columns 'gene','chr','start', and 'end', suitable for input to the setGeneTable function.

Note

At the time of package release, the BioMart community portal is temporarily unavailable. See www.biomart.org for updated status or more information. To access alternative hosts, pass additional arguments to the internal call to biomaRt::useMart(...), as in the second example below.

References

Durinck S., Spellman P.T., Birney E. and Huber W. (2009) Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt, Nature Protocols, 4, 1184–1191.

See Also

setGeneTable

Examples

## Not run: 
getBioMartData(c("BRCA1","BRCA2"))
getBioMartData(c("BRCA1","BRCA2"), 
               host="www.ensembl.org", 
               biomart="ENSEMBL_MART_ENSEMBL", 
               dataset="hsapiens_gene_ensembl")

## End(Not run)

snplist documentation built on Oct. 9, 2021, 5:06 p.m.