geome-db

A set of R scripts for accessing and working with geome-db FIMS data from R

Installation

To get the current released version from CRAN :

install.packages("geomedb")

To get the current development version from github:

install.packages("devtools")
library(devtools)
install_github("dipnet/fimsR-access")
library(geomedb)

Examples

The query function will execute a query against the fims database. The results are returned as a data.frame The most basic query will return all the samples in the database:

df <- queryMetadata()

The following query will return all samples for the expeditions “TEST” and “TEST2”

df <- queryMetadata(expeditions=list("TEST", "TEST2"))

The following query will the return “materialSampleID” and “bcid” columns for all samples.

df <- queryMetadata(names=list("materialSampleID", "bcid"))

The following query will the return “materialSampleID” and “bcid” columns for all samples where a full text search matches “Chordata”

df <- queryMetadata(names=list("materialSampleID", "bcid"), query="Chordata")

The following query will the return “materialSampleID” and “bcid” columns for the samples in “TEST” expeditions where “yearCollected” = 2008

df <- queryMetadata(expeditions=list("TEST"), names=list("materialSampleID", "bcid"), query="+yearCollected:2008")

The following will fetch “CO1” fasta sequences and return a DNABin

fasta <- queryFasta("C01", expeditions=list("TEST"), query="+yearCollected:2008")

You can fetch a list of expeditionCodes that are available to query:

expeditionsList <- listExpeditions()

You can fetch a list of the current fasta marker types:

markers <- listMarkers()