BIOMretrieval: Get annotation information of samples as BIOM data

Description

Retrieve annotation pipeline information (such as abundance profiles) for specified metagenomes and projects into an object of class biom.

Usage

biomRequest(x, request=c("function", "organism", "feature"), ...,  block, wait=TRUE, quiet=FALSE, file, outfile)
"biom"(x, wait=TRUE, ..., quiet=FALSE)

Arguments

a set of metagenomes and/or projects (character) or a request ticket (environment)

request

choice of annotation type (string)

...

arguments specifying or qualifying the data desired (biomRequest() only)

block

number of metagenomes per API call (integer)

wait

return only when data is complete? (logical)

quiet

suppress messages and warnings? (logical)

file

file containing a set of metagenomes or projects (string)

outfile

file to save the retrieved data (string)

Value

For biomRequest(), an environment if wait=FALSE. Otherwise and for biom.environment(), a biom object.

Details

Complete technical documentation is forthcoming. For the current preliminary release, please refer to the examples provided.

Examples

Run this code

####  several files demonstrate valid formats for ID input
demoSets()

## Not run: 
# ff <- demoSets()
# 
# ####  simple retrieval of annotation data
# yy <- biomRequest (file=ff[1])
# head (rows (yy))
# 
# ####  many arguments can modify what is retrieved
# yy <- biomRequest (file=ff[1], group_level="level1")
# rownames (yy)
# 
# ####  taxonomic annotations
# yy <- biomRequest (file=ff[4], request="organism", group_level="phylum", source="Greengenes")
# 
# ####  IDs can be given directly, while output can be to a file
# biomRequest ("mgp9", request="function", outfile="mgp9.biom")
# biomRequest ("mgm4441619.3 mgm4441620.3 mgm4441656.4", 
#   request="function", outfile="mgp9.biom")
# 
# ####  place an asynchronous request...
# yy <- biomRequest ("mgp9", wait=FALSE)
# ####  ...and receive the data when convenient
# yy <- biom (yy)
# ## End(Not run)

####  full detail for available options
doc.MGRAST (3, head=c("matrix","function","parameters","options"))
doc.MGRAST (3, head=c("matrix","organism","parameters","options"))
doc.MGRAST (3, head=c("matrix","feature","parameters","options"))