hoardeR (version 0.10)

getGeneSeq: Extracting a gene sequence from NCBI database.

Description

This function retrieves a gene sequence from the NCBI database.

Usage

getGeneSeq(chr, start, end, organism)

Value

A string that contains the genomic sequence.

Arguments

chr

Chromosome number, numeric/string

start

Start position, numeric

end

End position, numeric

organism

Name of the organism, string

Author

Daniel Fischer

Details

Extracting a gene sequence from NCBI database. For a list of available organism, visit

http://genome.ucsc.edu/cgi-bin/das/dsn. All id="." field are available.

Examples

if (FALSE) {
# Extracting for Sus Scrofa, build version 3:
getGeneSeq(1,2134,14532,"susScr3")
getGeneSeq(10,1233312,1233350,"hg38")
}