search.MGRAST: Find metagenomes matching specified criteria

In matR: Metagenomics Analysis Tools

Description

Find metagenomes matching search terms specified for metadata, annotations, and/or md5s, giving minimal or detailed metadata per metagenome.

Usage

search.MGRAST(public=NULL, detail=NULL, match.all=TRUE, ..., quiet=TRUE)

Arguments

public	optional restriction on sharing status (NULL or logical)
detail	level of metadata detail (NULL, TRUE, or character)
match.all	require match on all provided criteria? (logical)
...	arguments to call.MGRAST()
quiet	suppress messages and warnings? (logical)

Details

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

Value

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

Author(s)

Daniel T. Braithwaite

See Also

dir.MGRAST, metadata.character, MGRASTer::call.MGRAST

Examples

####  relevant documentation for the underlying API call
doc.MGRAST (3, head=c('metagenome','query','parameters','options'))

Example output

Loading required package: MGRASTer
MGRASTer (0.9 02e288)
Loading required package: BIOM.utils
BIOM.utils (0.9 dbcb27)
matR: metagenomics analysis tools for R (0.9 c71ee9)
List of 11
 $ verbosity:List of 2
  ..$ : chr "cv"
  ..$ :List of 5
  .. ..$ : chr [1:2] "minimal" "returns only minimal information"
  .. ..$ : chr [1:2] "mixs" "returns all GSC MIxS metadata"
  .. ..$ : chr [1:2] "metadata" "returns minimal with metadata"
  .. ..$ : chr [1:2] "stats" "returns minimal with statistics"
  .. ..$ : chr [1:2] "full" "returns all metadata and statistics"
 $ function : chr [1:2] "string" "search parameter: query string for function"
 $ status   :List of 2
  ..$ : chr "cv"
  ..$ :List of 3
  .. ..$ : chr [1:2] "both" "returns all data (public and private) user has access to view"
  .. ..$ : chr [1:2] "public" "returns all public data"
  .. ..$ : chr [1:2] "private" "returns private data user has access to view"
 $ match    :List of 2
  ..$ : chr "cv"
  ..$ :List of 2
  .. ..$ : chr [1:2] "all" "return metagenomes that match all search parameters"
  .. ..$ : chr [1:2] "any" "return metagenomes that match any search parameters"
 $ direction:List of 2
  ..$ : chr "cv"
  ..$ :List of 2
  .. ..$ : chr [1:2] "asc" "sort by ascending order"
  .. ..$ : chr [1:2] "desc" "sort by descending order"
 $ order    : chr [1:2] "string" "metagenome object field to sort by (default is id)"
 $ metadata : chr [1:2] "string" "search parameter: query string for any metadata field"
 $ limit    : chr [1:2] "integer" "maximum number of items requested"
 $ md5      : chr [1:2] "string" "search parameter: md5 checksum of feature sequence"
 $ organism : chr [1:2] "string" "search parameter: query string for organism"
 $ offset   : chr [1:2] "integer" "zero based index of the first data object to be returned"

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