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Package matR (metagenomics analysis tools for R) is an analysis client for the MG-RAST metagenome annotation engine, part of the US Department of Energy (DOE) Systems Biology Knowledge Base (KBase). Customized statistical and visualization tools securely access remote data and metadata. See: http://metagenomics.anl.gov and: http://kbase.us

LOADING During an R session, load matR with:

library(matR)

INSTALLATION Make sure to have a current version of the R language (http://www.r-project.org). Then install during an R session with:

install.packages(matR) library(matR) dependencies()

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Version

Install

install.packages('matR')

Monthly Downloads

10

Version

0.9

License

BSD_2_clause + file LICENSE

Issues

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Maintainer

Daniel Braithwaite

Last Published

October 23rd, 2014

Functions in matR (0.9)

BIOMannotations

Search and change row or column annotations of BIOM data
getMetRows

Get single field from row metadata
dependencies

Install recommended packages
step.through

Step through a demo line-by-line
BIOMrename

Change row and column identifiers of BIOM data
dir.MGRAST

List directory of projects
demoObjects

BIOM annotation data for certain metagenomes and projects
buildDemoSets

Build objects containing metagenome annotations as BIOM data
parAuto

Provide automatic par values
metadata.character

Get metadata of projects and metagenomes
demoSets

Get paths to files of metagenome and project IDs
parMap

Determine par values according to a provided metadata mapping
distx

Calculate distances with optional grouping and other features
IDsets

Handle sets of metagenome and project IDs
image.biom

Display heatmap of BIOM data with optional dendrograms
hazPackages

Check for presence of recommended packages
transform.biom

Apply mathematical transformations to BIOM data
BIOMmerge

Merge BIOM data
BIOMsubset

Take part of (subset) BIOM data
rowstats

Apply selected significance test across rows
subMetadata

Substitute for reference to row or column metadata
stepper

Step through a demo line-by-line
search.MGRAST

Find metagenomes matching specified criteria
getMetColumns

Get single field from column metadata
princomp.biom

Compute and plot principal coordinates of BIOM data
boxplot.biom

Summarize BIOM data in boxplots
BIOMretrieval

Get annotation information of samples as BIOM data
collapse

Collapse character vectors to a single string