matR: Metagenomics Analysis Tools for R
Version 0.9

An analysis platform for metagenomics combining specialized tools and workflows, easy handling of the BIOM format, and transparent access to MG-RAST resources. matR integrates easily with other R packages and non-R software.

Browse man pages Browse package API and functions Browse package files

AuthorDaniel Braithwaite [aut, cre], Kevin Keegan [aut], University of Chicago [cph]
Date of publication2014-10-23 11:50:13
MaintainerDaniel Braithwaite <contact.dtb@gmail.com>
LicenseBSD_2_clause + file LICENSE
Version0.9
URL https://github.com/MG-RAST/matR/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("matR")

Man pages

BIOMannotations: Search and change row or column annotations of BIOM data
BIOMmerge: Merge BIOM data
BIOMrename: Change row and column identifiers of BIOM data
BIOMretrieval: Get annotation information of samples as BIOM data
BIOMsubset: Take part of (subset) BIOM data
boxplot.biom: Summarize BIOM data in boxplots
buildDemoSets: Build objects containing metagenome annotations as BIOM data
collapse: Collapse character vectors to a single string
demoObjects: BIOM annotation data for certain metagenomes and projects
demoSets: Get paths to files of metagenome and project IDs
dependencies: Install recommended packages
dir.MGRAST: List directory of projects
distx: Calculate distances with optional grouping and other features
getMetColumns: Get single field from column metadata
getMetRows: Get single field from row metadata
hazPackages: Check for presence of recommended packages
IDsets: Handle sets of metagenome and project IDs
image.biom: Display heatmap of BIOM data with optional dendrograms
metadata.character: Get metadata of projects and metagenomes
parAuto: Provide automatic par values
parMap: Determine par values according to a provided metadata mapping
princomp.biom: Compute and plot principal coordinates of BIOM data
rowstats: Apply selected significance test across rows
search.MGRAST: Find metagenomes matching specified criteria
stepper: Step through a demo line-by-line
step.through: Step through a demo line-by-line
subMetadata: Substitute for reference to row or column metadata
transform.biom: Apply mathematical transformations to BIOM data

Functions

IDsets Man page
[.biom Man page
abbrev Source code
ast.lib Source code
biom.environment Man page Source code
biomRequest Man page Source code
boxplot Man page
boxplot.biom Man page Source code
buildDemoSets Man page Source code
buildHTMLDocs Source code
collapse Man page Source code
columns Man page Source code
columns<- Man page
demoObjects Man page
demoSets Man page Source code
dependencies Man page Source code
dimnames<-.biom Man page
dir.MGRAST Man page Source code
distx Man page Source code
distx.biom Man page Source code
distx.matrix Man page Source code
expandSet Man page Source code
getMetColumns Man page Source code
getMetRows Man page Source code
hazPackages Man page Source code
image Man page
image.biom Man page Source code
insertHelper Source code
list2df Source code
merge.biom Man page Source code
metadata Man page
metadata.character Man page Source code
onAttach Source code
parAuto Man page Source code
parMap Man page Source code
princomp Man page
princomp.biom Man page Source code
randomize.matrix Source code
readSet Man page Source code
resolve Source code
rows Man page Source code
rows<- Man page
rowstats Man page Source code
rowstats.biom Man page Source code
rowstats.matrix Man page Source code
scrapeSet Man page Source code
scrubSet Man page Source code
search.MGRAST Man page Source code
seeDoc Source code
step.through Man page Source code
stepper Man page Source code
stepper2 Source code
subColumn Man page Source code
subRow Man page Source code
t_ColCenter Man page Source code
t_ColScale Man page Source code
t_DENorm Source code
t_Log Man page Source code
t_NA2Zero Man page Source code
t_Threshold Man page Source code
tagline Source code
transform Man page
transform.biom Man page Source code
warning Source code
xx1 Man page
xx2 Man page
xx3 Man page
xx4 Man page
yy1 Man page
yy2 Man page
yy3 Man page
yy4 Man page

Files

inst
inst/extdata
inst/extdata/set-4.tsv
inst/extdata/set-6.tsv
inst/extdata/set-1.tsv
inst/extdata/set-7.tsv
inst/extdata/set-2.tsv
inst/extdata/set-3.tsv
inst/extdata/set-5.tsv
tests
tests/data-test.R
tests/graphics-test.R
tests/analysis-test.R
tests/client-test.R
tests/input-form-test.R
tests/biom-ext-test.R
NAMESPACE
demo
demo/simple.R
demo/functions.R
demo/00Index
demo/ant.R
demo/API.R
demo/whyR.R
data
data/demoObjects.rda
R
R/utils.R
R/graphics.R
R/boxplot.R
R/biom-ext.R
R/analysis-support.R
R/init.R
R/client.R
R/image.R
R/princomp.R
R/distx.R
R/analysis-misc.R
R/transform.R
R/rowstats.R
README.md
MD5
DESCRIPTION
man
man/distx.Rd
man/demoObjects.Rd
man/getMetColumns.Rd
man/BIOMsubset.Rd
man/parAuto.Rd
man/BIOMannotations.Rd
man/BIOMrename.Rd
man/search.MGRAST.Rd
man/stepper.Rd
man/BIOMmerge.Rd
man/dependencies.Rd
man/hazPackages.Rd
man/getMetRows.Rd
man/buildDemoSets.Rd
man/subMetadata.Rd
man/IDsets.Rd
man/demoSets.Rd
man/dir.MGRAST.Rd
man/metadata.character.Rd
man/transform.biom.Rd
man/step.through.Rd
man/boxplot.biom.Rd
man/image.biom.Rd
man/collapse.Rd
man/BIOMretrieval.Rd
man/parMap.Rd
man/rowstats.Rd
man/princomp.biom.Rd
LICENSE
matR documentation built on May 19, 2017, 11:39 a.m.