querySanger | R Documentation |
For Sanger sequence data (typically of mitochondrial origin), it is possible to store the sequence directly within GEOME. 'querySanger()' allows you to download this sequence data into a DNAbin object, as well as to your working directory as a FASTA-formatted file.
querySanger(locus, projects = list(), expeditions = list(), query = "")
locus |
the locus to fetch. list of markers can be found by calling 'listLoci()' |
projects |
list of projects to include in the query. The default is all projects |
expeditions |
Only applicable if projects are specified. list of expeditions to include in the query. The default is all expeditions |
query |
FIMS Query DSL http://fims.readthedocs.io/en/latest/fims/query.html query string. Ex. 'yearCollected >= 2017 and country = "Indonesia"' |
a DNAbin object, which is a fairly standard form for storing DNA data in binary format. It will also download a FASTA-formatted file to your working directory.
## Not run: data <- querySanger( locus = 'CYB', projects=list(1), expeditions=list("acaach_CyB_JD", "acajap_CyB_JD"), query="yearCollected >= 2008") data <- querySanger(locus = 'CO1', query = "genus = Linckia AND specificEpithet = laevigata" ) ## End(Not run)
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