R for Amplicon-Sequencing-Based Microbial-Ecology

Documentation for package ‘RAM’ version 1.2.1.7

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Analysis of Amplicon-Based Metagenomic Data

-- A --

alignment	Sample Alignment
assist.ado	Perform ADONIS Analysis for OTU Tables Or Taxonomic Abundance Matrix
assist.cca	Perform CCA and RDA Analysis for OTU Tables
assist.NB	Negative Binomial Test For OTUID or Taxon
assist.ordination	Perform CCA and RDA Analysis for OTU Tables
assist.rda	Perform CCA and RDA Analysis for OTU Tables

-- C --

col.splitup	Split Column Of Data Frame
combine.OTU	Combine Non Overlapped OTU tables From The Same Community
core.OTU	Summary Of Core OTUs
core.OTU.rank	Summary Of Core OTUs
core.Taxa	Show Summary of Core Taxa
correlation	Plot Of Correlation Coefficient

-- D --

data.clust	Plot Hierarchical Cluster Of Samples Based on OTU Table or Taxonomic Abundance Matrix
data.revamp	Transform OTU Table
data.subset	Subset OTU And Metadata
dissim	Calculate Dissimilarity Matrix Data
dissim.alleig.plot	Plot Dissimilarity Matrix Data for Different Methods
dissim.clust	Calculate Dissimilarity Matrix Data
dissim.clust.plot	Plot Dissimilarity Matrix Data for Different Methods
dissim.eig	Calculate Dissimilarity Matrix Data
dissim.eig.plot	Plot Dissimilarity Matrix Data for Different Methods
dissim.GOF	Calculate Dissimilarity Matrix Data
dissim.GOF.plot	Plot Dissimilarity Matrix Data for Different Methods
dissim.heatmap	Plot Distance Matrix Heatmap for OTU Samples
dissim.ord	Calculate Dissimilarity Matrix Data
dissim.ord.plot	Plot Dissimilarity Matrix Data for Different Methods
dissim.plot	Plot Dissimilarity Matrix Data for Different Methods
dissim.pvar	Calculate Dissimilarity Matrix Data
dissim.pvar.plot	Plot Dissimilarity Matrix Data for Different Methods
dissim.tree	Calculate Dissimilarity Matrix Data
dissim.tree.plot	Plot Dissimilarity Matrix Data for Different Methods
diversity.indices	Calculate True Diversity and Evenness

-- E --

envis.NB	Visualize The Negative Binomial Model OF A Given Taxon OR OTUID
evenness	Calculate True Diversity and Evenness

-- F --

factor.abundance	Plot the Abundance of OTUs by Classification at a Given Taxonomic Rank For Each Level of A Metadata Category Variable.
filter.META	Select METADATA Variables
filter.OTU	Filter OTU
filter.Taxa	Filter Taxonomic Abundance Matrix by Total Counts Or Maximum Relative Abundance
fread.meta	Load Metadata Table
fread.OTU	Fast Load Large OTU Table

-- G --

get.rank	Get OTUs Classified at Taxonomic Rank(s)
group.abund.Taxa	Barplot Of Distribution Of Taxa In Groups
group.abundance	Plot the Abundance of OTUs by Classification at a Given Taxonomic Rank
group.abundance.meta	Plot the Abundance of OTUs by Classification at a Given Taxonomic Rank
group.diversity	Boxplot To Compare Diversity Indices Among Groups
group.heatmap	Plot OTU Abundance at a Given Rank with Metadata Annotation
group.heatmap.simple	Plot a Heatmap Showing OTU Abundance by Taxonomic Classification
group.indicators	Plot Indicator Taxon Groups for Metadata Trends
group.OTU	Plot Distribution of OTUs
group.rich	Barplot Of Richness For Each Level Of A Given Metadata Variable
group.spatial	Plot Spatial Collection Trends for Taxon Groups
group.spec	Boxplot Of Richness For Each Level Of A Given Metadata Variable
group.Taxa.bar	Barplot Of Taxa Distribution In Groups
group.Taxa.box	Boxplot Of Taxa In Each Level of A Metadata Variable
group.temporal	Plot Temporal Trends for Metadata and Taxon Groups
group.top.number	Plot the Top Taxon Groups
group.top.percent	Plot the Top Taxon Groups
group.venn	Plot Venn Diagram For Two To Five Sets With Item Labels

-- I --

-- L --

LCA.OTU	Lowest Common Ancestor (LCA) OF EACH OTU
location.formatting	Location Formatting

-- M --

match.data	Match Samples In Ecology Data Sets and Metadata
meta	Sample Metadata for ITS1/ITS2
META.clust	Plot Hierarchical Cluster Of Metadata

-- N --

Creates Nodes and Edge-List For An OTU Table

-- O --

OTU.cca	Ordination Plot For OTUs Using CCA or RDA Analysis
OTU.diversity	Summarize Diversity Indices for OTU Tables
OTU.ord	Ordination Plot For OTUs Using CCA or RDA Analysis
OTU.rarefy	Create Rarefied OTU Tables
OTU.rda	Ordination Plot For OTUs Using CCA or RDA Analysis
OTU.recap	Summarize OTU

-- P --

pcoa.plot	Create a PCoA plot for an OTU Table
percent.classified	Calculate Percent of OTUs Classified at a Given Taxonomic Rank
phylog_taxonomy	Plot Hierarchical Taxonomic Tree
phylo_taxonomy	Plot Hierarchical Taxonomic Tree with Relative Abundance

-- R --

RAM	Analysis of Amplicon-Based Metagenomic Data
RAM.border	Customized Themes For GGPLOT
RAM.color	Customized Themes For GGPLOT
RAM.dates	Date Formatting for RAM
RAM.factors	Factor Formatting for RAM
RAM.input.formatting	Data Input Formatting
RAM.pal	Creat Color Palette
RAM.plotting	Creating Plots with RAM
RAM.rank.formatting	Taxonomic Rank Formatting
read.meta	Open Metadata Table
read.OTU	Open OTU Table
reformat.taxonomy	Validate And Reformat The OTU Taxonomy Column
reset.META	Reset OTU

-- S --

sample.locations	Plot the Geographic Location of Samples
sample.map	Plot The Geographic Location of Samples
sample.sites	Plot The Geographic Location of Samples
seq_var	Plot Intra And Inter Specific Variation For An Alignment
shared.OTU	Summary of Shared OTUs Across ALL Subjects
shared.Taxa	Summary of Shared Taxa Across ALL Subjects

-- T --

tax.abund	Aggregate OTU Data Based on Taxonomy
tax.fill	Fill Missing Taxonomic Information
tax.split	Split OTU Tables By Taxonomic Rank
Taxa.cca	Ordination Plot For Taxa Groups Using CCA or RDA Analysis
Taxa.ord	Ordination Plot For Taxa Groups Using CCA or RDA Analysis
Taxa.rda	Ordination Plot For Taxa Groups Using CCA or RDA Analysis
top.groups.plot	Plot the Top Taxon Groups
transpose.LCA	Transpose OTU Tables With LCA Annotation For Each OTU
transpose.OTU	Take the Transpose of an OTU Table
true.diversity	Calculate True Diversity and Evenness

-- V --

valid.OTU	Validate an OTU Table
valid.taxonomy	Validate And Reformat The OTU Taxonomy Column

-- W --

Write Data To CSV File