getKEGGGeneSeq: Get protein and gene sequences

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/getKEGG.R

Description

KEGG Database API - Get the nucleotide acid and amino acid sequences

Usage

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getKEGGGeneSeq(KEGGID, seqType = "aaseq", n = 4)

Arguments

KEGGID

A vector of KEGG IDs. Seqences from different species could be combined together.

seqType

Choose nucleotide acid (ntseq) or amino acid (aaseq) seqences, and the default is amino acid sequences.

n

The number of CPUs or processors, and the default value is 4.

Details

Get the protein and gene sequences in fasta format. This function support mutiple querys.

Value

A BStringSet

Author(s)

Yulong Niu [email protected]

References

http://www.kegg.jp/kegg/rest/keggapi.html

See Also

getKEGGTIDGeneSeq

Examples

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# two amino acid seqences from different sepecies with 2 threads.
twoAASeqs <- getKEGGGeneSeq(c('mja:MJ_0011', 'hsa:10458'), n = 2)
## Not run: 
# export fasta format files
require('Biostrings')
writeXStringSet(twoAASeqs, 'twoAASeqs.fasta')
## End(Not run)

## Not run: 
# more examples
twoNTSeqs <- getKEGGGeneSeq(c('shy:SHJG_7159', 'shy:SHJG_7160'), 'ntseq')
mutilAASeqs <- getKEGGGeneSeq(c('eco:b0202', 'eco:b0203', 'eco:b0204',
'eco:b0205', 'eco:b0206', 'eco:b0216', 'eco:b0244',
'eco:b4626', 'eco:b3796', 'eco:b3797', 'eco:b3296',
'eco:b3297'))
## End(Not run)

## Not run: 
# get the whole E.coli genome protein seqences
ecoProIDs <- getProID('eco')
ecoGenomePro <- getKEGGGeneSeq(ecoProIDs[, 1])
## End(Not run)

YulongNiu/KEGG_BioCyc_API documentation built on June 3, 2017, 10:45 a.m.