geomedb (version 2.0.1)

querySanger: Query Sanger sequences directly from the GEOME database

Description

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.

Usage

querySanger(locus, projects = list(), expeditions = list(),
  query = "")

Arguments

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"'

Value

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.

Examples

# 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" )
# }