rplant-package: rplant

In rPlant: Interface to the Agave API

Description

R interface to iPlant's Discovery Enviornment and the Taxonomic Name Resolution Service (TNRS)

Details

The iPlant Collaborative has developed many resources to deal with the emerging computational challenges facing biology. Users have access to many different applications for data analysis, including clustering/network analyses, QTL mapping, sequence alignments, phylogenetic tree building, and comparative methods. The 'rPlant' package provides a direct link between iPlant's API and the R environment. 'rPlant' users must be registered with iPlant and have a valid user name and password. If you do not have an account yet, visit http://user.iplantcollaborative.org/ and register.

Package:	rplant
Type:	Package
Version:	3.0.0
Date:	2014-6-5
License:	GPL (>= 2)

See Also

Validate, UploadFile, Muscle

Examples

## Not run: data(PROTEIN.fasta)
## Not run: write.fasta(sequences = PROTEIN.fasta, names = names(PROTEIN.fasta), 
                     file.out = "PROTEIN.fasta")
## End(Not run)
## Not run: Validate("username","password")
## Not run: UploadFile("PROTEIN.fasta", filetype="FASTA-0")
## Not run: SubmitJob(application="Muscle-3.8.32u4", file.list=list("PROTEIN.fasta"), 
                   input.list=list("stdin"), args.list=list(c("arguments", "-phyiout")),
                   job.name="MuscleSJAA")
## End(Not run)

### Or, one can use one of the wrapper functions. ###
## Not run: Muscle("PROTEIN.fasta", aln.filetype="PHYLIP_INT", job.name="muscleAA")

rPlant documentation built on April 14, 2017, 6:03 p.m.