RAM-package: Analysis of Amplicon-Based Metagenomic Data

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

The RAM package provides a series of functions to make amplicon based metagenomic analysis more accessible. The package is designed especially for those who have little or no experience with R. This package calls heavily upon other packages (such as vegan and ggplot2), but the functions in this package either extend their functionality, or increase the ease-of-use.

Details

Package:	RAM
Type:	Package
Version:	1.2.0
Date:	2014-12-10
License:	MIT License, Copyright (c) 2014 Government of Canada

Load data from .csv-formatted OTU files with read.OTU or fread.OTU, then process the data with other commands. Type the command library(help = RAM) for a full index of all help topics, or ls("package:RAM") to get a list of all functions in the package. Type data(ITS1, ITS2, meta) to load sample data sets of RAM, which include the following data of 16 samples: 1) ITS1: OTU table of fungal internal transcribed spacer region1 3) ITS2: OTU table of fungal internal transcribed spacer region2 3) meta: associated metadata 4) alignment for seq_var Type citation("RAM") for how to cite this package. This pacakge contains information licensed under the Open Government Licence - Canada. See group.spatial for further details.

Author(s)

Wen Chen and Joshua Simpson. Maintainer: Wen Chen <[e-mail]>

See Also

vegdist, ggplot

Examples

## Not run: 
# load data from your own files...
otu1 <- fread.OTU("path/to/OTU/table")
otu2 <- read.OTU("path/to/OTU/table")
meta1 <- fread.meta("path/to/meta/table")
meta2 <- read.meta("path/to/meta/table")
# ...or use the included sample data
data(ITS1, ITS2, meta)
data <- list(ITS1=ITS1, ITS2=ITS2)
dissim.heatmap(ITS1, meta, row.factor=c(City="City"))
dissim.alleig.plot(data)
data(alignment)
# type library(help = RAM) to get a full listing of help 
documents

## End(Not run)

RAM documentation built on May 2, 2019, 3:04 p.m.