getSequence {biomaRt}R Documentation

Retrieves sequences

Description

This function retrieves sequences given the chomosome, start and end position. For genomic sequences the strand that is returned is the 5' t0 3' strand. Note that using this function with MySQL is limited to genomic sequences.

Usage

getSequence( chromosome, start, end, id, type, seqType, mart)

Arguments

chromosome Chromosome name
start start position of sequence on chromosome
end end position of sequence on chromosome
id An identifier or vector of identifiers.
type The type of identifier used. Supported types are hugo, ensembl, embl, entrezgene, refseq, ensemblTrans and unigene.
seqType Type of sequence that you want to retrieve. Allowed seqTypes are: cdna, peptide, 3utr, 5utr, genomic
mart object of class Mart, containing connections to the BioMart databases. You can create such an object using the function useMart.

Author(s)

Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck

Examples

if(interactive()){
mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl")

seq = getSequence(id="BRCA1", type="hugo", seqType="peptide", mart = mart)
show(seq)

martDisconnect(mart = mart)
}

[Package biomaRt version 1.8.2 Index]