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()