metadata.character: Get metadata of projects and metagenomes

In matR: Metagenomics Analysis Tools

Description

Get metadata of projects or metagenomes specified by ID, or simply look up correspondence of project and metagenome IDs.

Usage

## S3 method for class 'character'
metadata(x, detail=NULL, ..., quiet=TRUE, file)

Arguments

x	IDs of projects or metagenomes (character)
detail	level of metadata detail (NULL, TRUE, or character)
...	arguments to call.MGRAST()
quiet	suppress messages and warnings? (logical)
file	file containing project or metagenome IDs (string)

Details

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

Value

A list (for projects) or vector (for metagenomes) when detail=NULL. Otherwise, a data.frame.

Note

The function metadata() is declared S3 generic in required package BIOM.utils, and a method is defined there for class biom. Although here is documented another method of the same function, the actual functionality is unrelated.

Author(s)

Daniel T. Braithwaite

See Also

dir.MGRAST, search.MGRAST, biomRequest, MGRASTer::call.MGRAST

Examples

## Not run: 
####  three levels of detail for project metadata
xx <- "mgp21 mgp24 mgp30"
metadata (xx)
metadata (xx, detail=TRUE)
names (metadata (xx, detail="verbose"))

####  similar (but not identical) for metagenome metadata
yy <- "mgm4440066.3 mgm4440062.3 mgm4440055.3 mgm4441681.3 mgm4440463.3 mgm4440464.3"
metadata (yy)
metadata (yy, detail=TRUE)
names (metadata (yy, detail="metadata"))

## End(Not run)

####  relevant documentation for underlying API calls
doc.MGRAST (3, head=c('project','instance','parameters','options'))
doc.MGRAST (3, head=c('metagenome','instance','parameters','options'))

matR documentation built on May 2, 2019, 6:53 a.m.