R: Retrieve Resources from the Kbase MG-RAST Server

kbGet {KbaseKit}

R Documentation

Retrieve Resources from the Kbase MG-RAST Server

Usage

kbGet(ID, resource, namespace = NULL, annoType = NULL, seqType = NULL, org = NULL, func = NULL, md5 = NULL, param = NULL, toFile = NULL)

Arguments

`ID`	An ID appropriate to the resource requested
`resource`	One of `"project"`, `"sample"`, `"library"`, `"metagenome"`, `"subset"`, `"sequenceSet"`, `"sequences"`, `"reads"`, `"abundance"`
`namespace`
`annoType`
`seqType`
`org`
`func`
`md5`
`param`
`toFile`

Details

Where appropriate, parameters may hold (indifferently) either numeric or character values. Also, a single parameter is often allowed to carry multiple values. Multiple values may be passed within a vector or semicolon-separated character string. Accordingly, these are all valid values for the ID parameter:
123
"123"
c(123,456)
c("123","456")
"123;456"
c(123,"456;789")
Similar usage is allowed, depending on the resource requested, within the namespace, org, func, and md5 parameters.

If kbGet does not function properly, the authorization key may need to be reset. See Kbase Authorization.

Author(s)

Daniel Braithwaite

Examples

P <- kbGet( 92, "project" )
L <- kbGet( 3482.4, "library" )
S <- kbGet( 441, "sample" )
M <- kbGet( "4447971.3", "metagenome" )
sub <- kbGet( "4447971.3", "subset", org="Abiotrophia%20defectiva%20ATCC%2049176" )
seq <- kbGet( "4441602.3", "sequences", md5="5c6cdf00b3b2509879f412d55582af1a" )
M1 <- kbGet( c(4443360.3,4443361.3,4443362.3), "abundance", namespace="SEED" )
M2 <- kbGet( "4443360.3;4443361.3;4443362.3", "abundance", namespace="SEED", toFile="myfile" )
M3 <- kbGet("4443360.3;4443361.3;4443362.3", "abundance", namespace="SEED", param="format/plain" )