getMgrastAnnotation: Get the annotation profile from MGRAST

In mmnet: A metagenomic pipeline for systems biology

Description

The function downloads the annotation profile in MGRAST

Usage

getMgrastAnnotation(MetagenomeID, evalue = 5, identity = 60, length = 15, resource = c(source = "KO", type = "ontology"), login.info = NULL)

Arguments

MetagenomeID	character, the metagenome ID in mgrast
evalue	expectation negative exponent value threshold for saving hits, default is 5
identity	minimum percent identity of matches, default is 60
length	value for minimum alignment length cutoff, default is 15
resource	a two length vecter, the source you want to download, e.g., c("KO","ontology") represents the ontology annotation with the KO database , more details in MGRAST
login.info	a list of login info generated after user login into MGRAST which consists of webkey of the file, the invlid time of your webkey, cookie, websession and curlhandle. It is unique for each users

Value

annotation profile

References

http://api.metagenomics.anl.gov/1/api.html#annotation

Examples

##
# getMgrastAnnotation("mgm4447943.3")

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: biom

mmnet documentation built on May 31, 2017, 3:25 p.m.