getSequence {biomaRt} | R Documentation |
This function retrieves sequences given the chomosome, start and end position
getSequence( species, chromosome, start, end, martTable, mart)
species |
Species information. A list of possible values for this argument can be obtained by the function getSpecies. |
chromosome |
Chromosome name |
start |
start position of sequence on chromosome |
end |
end position of sequence on chromosome |
martTable |
alternatively a martTable can be used containing all information |
mart |
object of class Mart, containing connections to the BioMart databases. You can creat such an object using the function martConnect. |
Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck
if(interactive()){ mart <- martConnect(biomarts = c("ensembl","sequence")) seq = getSequence(species="ggallus", chromosome = 1, start = 400, end = 500, mart = mart) show(seq) martDisconnect(mart = mart) }