Package 'OTUbase' reference manual

Title:	Provides structure and functions for the analysis of OTU data
Description:	Provides a platform for Operational Taxonomic Unit based analysis
Authors:	Daniel Beck, Matt Settles, and James A. Foster
Maintainer:	Daniel Beck <[email protected]>
License:	Artistic-2.0
Version:	1.55.0
Built:	2024-07-12 04:48:38 UTC
Source:	https://github.com/bioc/OTUbase

The OTUbase package: A tool for organizing and manipulating Operational Taxonomic Unit data

Description

The OTUbase Base class for OTU data

Details

Package:	OTUbase
Type:	Package
Version:	0.1.0
Date:	2010-04-05
License:	Artistic-2.0
LazyLoad:	yes

~~OTUbase includes a number of OTUset type classes which provide structure for OTU based data. These classes allow the user to store information that may be usefull in the analysis of OTUs. Slots are provided for sequence and quality values, OTU classifications, Sample identifications, and metadata associated with samples and OTUs. In addition, basic functions are provided for the analysis and visualization of the data. In addition to OTU type analysis, classification data is also supported with the TAXset classes.~~

Author(s)

Daniel Beck - [email protected], Matt Settles - [email protected], and James Foster Maintainer: Daniel Beck - [email protected]

References

An_introduction_to_OTUbase.pdf

"OTUset" class for OTU data

Description

This class provides a way to store and manipulate operational taxonomic unit data. ".OTUset" is inherited by "OTUsetQ", "OTUsetF", and "OTUsetB". The user will want to use "OTUsetQ" when quality data is available, "OTUsetF" when sequence data (without quality data) is available, and "OTUsetB" when only OTU and sample data are available.

Slots

OTUsetB includes Slots id, sampleID, otuID, sampleData, assignmentData.

OTUsetF includes Slots id sampleID, otuID, sampleData, assignmentData, sread.

OTUsetQ includes Slots id sampleID, otuID, sampleData, assignmentData, sread, quality.

Methods

Methods include:

id: provides access to the id slot of object
sampleID: provides access to the sampleID slot of object
otuID: provides access the otuID slot of object
sampleData: provides accesss the sampleData slot of object
assignmentData: provides access the assignmentData slot of object
sread: provides access to the sread slot of object
quality: provides access to the quality slot of object
seqnames: returns the first word of the id line. Intended to extract the sequence name from other sequence information.
nsamples: returns the number of samples in an OTUset object
notus: returns the number of OTUs in an OTUset object
show: signature(object=".OTUset"): provides a brief summary of the object, including its class, number of sequences, number of samples, and number of OTUs.

Examples

showClass(".OTUset")
showMethods(class=".OTUset")
showClass("OTUsetQ")
showClass(".OTUset")
showMethods(class=".OTUset")
showClass("OTUsetQ")

"TAXset" class for TAX data

Description

This class provides a way to store and manipulate read-classification data. ".TAXset" is inherited by "TAXsetQ", "TAXsetF", and "TAXsetB". The user will want to use "TAXsetQ" when quality data is available, "TAXsetF" when sequence data (without quality data) is available, and "TAXsetB" when only classification and sample data are available.

Slots

TAXsetB includes Slots id, sampleID, tax, sampleData, assignmentData.

TAXsetF includes Slots id sampleID, tax, sampleData, assignmentData, sread.

TAXsetQ includes Slots id sampleID, tax, sampleData, assignmentData, sread, quality.

Methods

Methods include:

id: provides access to the id slot of object
sampleID: provides access to the sampleID slot of object
tax: provides access the tax slot of object
sampleData: provides accesss the sampleData slot of object
assignmentData: provides access the assignmentData slot of object
sread: provides access to the sread slot of object
quality: provides access to the quality slot of object
seqnames: returns the first word of the id line. Intended to extract the sequence name from other sequence information.
nsamples: returns the number of samples in an TAXset object
show: signature(object=".TAXset"): provides a brief summary of the object, including its class, number of sequences, and number of samples.

Examples

showClass(".TAXset")
showMethods(class=".TAXset")
showClass("TAXsetQ")
showClass(".TAXset")
showMethods(class=".TAXset")
showClass("TAXsetQ")

abundance

Description

abundance generates an abundance table. This table can be either weighted or unweighted.

Usage

abundance(object, ...)
abundance(object, ...)

Arguments

`object`	An OTUset or a TAXset object
`...`	Additional arguments. These will depend on if the object is an OTUset or a TAXset object.

Details

These are other arguments passed to abundance

taxCol If generating the abundance from a TAXset object, taxCol selects the column of the tax dataframe from which to calculate the abundance.
assignmentCol If generating the abundance from an OTUset object assignmentCol will select a column of the assignmentData dataframe to use when calculating abundance. This will override the default of creating an abundance table of the OTUs and instead create an abundance table of a column in the assignmentData dataframe.
sampleCol sampleCol generates the abundance table using a column in the sampleData data fram instead of the default of using the sampleID.
collab An optional parameter that selets a column of the sampleData dataframe to use when labeling the columns of the abundance table.
weighted By default this is FALSE. When set to TRUE abundance will return proportional abundances.

Value

The returned value will be a data.frame.

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## calculate abundance
abundance(soginOTU, collab="Site")
## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## calculate abundance
abundance(soginOTU, collab="Site")

Accessor functions for OTUset and TAXset objects

Description

These functions provide access to some of the slots of OTUset and TAXset objects. otuID returns the otuID slot of OTUset objects. sampleID returns the sampleID slot of both OTUset and TAXset objects. tax and tax<- return and replace the tax slot of TAXset objects.

Usage

    sampleID(object, ...)
    otuID(object, ...)
    tax(object, ...)
    tax(object)<-value
sampleID(object, ...)
    otuID(object, ...)
    tax(object, ...)
    tax(object)<-value

Arguments

`object`	An OTUset or a TAXset object
`value`	The replacement value for `tax`
`...`	Added for completeness. Enables the passing of arguments.

Value

sampleID and otuID return a character. tax returns a data.frame.

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get the sampleID slot
sampleID(soginOTU) 

## get the otuID slot
otuID(soginOTU)

## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get the sampleID slot
sampleID(soginOTU) 

## get the otuID slot
otuID(soginOTU)

assignmentData

Description

These accessors access and replace the assignmentData slot of OTUbase objects. assignmentData is an AnnotatedDataFrame. assignmentData and assignmentData<- access and replace this AnnotatedDataFrame. assignmentLabels and assignmentLabels<- access and replace the labels of this AnnotatedDataFrame. aData and aData<- access and replace the dataframe component of the AnnotatedDataFrame.

assignmentNames returns the assignment names present in the assignmentData slot.

Usage


    aData(object,...)
    aData(object)<-value
    assignmentData(object,...)
    assignmentData(object)<-value
    assignmentLabels(object,...)
    assignmentLabels(object)<-value
    assignmentNames(object,...)

aData(object,...)
    aData(object)<-value
    assignmentData(object,...)
    assignmentData(object)<-value
    assignmentLabels(object,...)
    assignmentLabels(object)<-value
    assignmentNames(object,...)

Arguments

`object`	An OTUset or a TAXset object
`value`	The replacement value for `assignmentData` or `assignmentLabels`
`...`	Added for completeness. Enables the passing of arguments.

Value

aData returns a dataframe. assignmentData returns an AnnotatedDataFrame. assignmentLabels returns a character. assignmentNames returns a character.

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get the aData dataframe
aData(soginOTU)

## get the assignmentData slot
assignmentData(soginOTU)

## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get the aData dataframe
aData(soginOTU)

## get the assignmentData slot
assignmentData(soginOTU)

clusterSamples

Description

This function is a wrapper for the vegan function vegedist and hclust. It allows the user to cluster samples using a number of different distance measure and clustering methods. Please see the documentation for vegedist and hclust for a more indepth explanation.

Usage

    clusterSamples(object, ...)
clusterSamples(object, ...)

Arguments

`object`	An OTUset or a TAXset object
`...`	Additional arguments. These will depend on if the object is an OTUset or a TAXset object.

Details

These are other arguments passed to clusterSamples. For further information on specific arguments, please see abundance, vegdist, or hclust.

taxCol Column of the tax slot dataframe on which to cluster (unique to TAXset objects). Passed to the abundance function.
assignmentCol Column of the assignmentData dataframe used to classify sequences for clustering. This overrides the default of using the OTUs to cluster samples. This is passed to the abundance function.
collab Specifies a column of the sampleData dataframe that will provide the sample lables for the cluster analysis. This is passed to the abundance function.
distmethod The distance method to be used. This value is passed to the vegedist function. The default is the Bray-Curtis distance.
clustermethod The clustering method to be used. This value is passed to the hclust function. The default is complete clustering.

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## cluster samples
clusterSamples(soginOTU, collab="Site", distmethod="jaccard")

## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## cluster samples
clusterSamples(soginOTU, collab="Site", distmethod="jaccard")

Other functions

Description

These are other functions available. Caution is advised when using them. Some are still in development and others only work on specific objects (OTUset or TAXset).

Usage

    getOTUs(object, colnum, value, exact)
    getSamples(object, colnum, value, exact)
    o_diversity(object, ...)
    o_estimateR(object, ...)
getOTUs(object, colnum, value, exact)
    getSamples(object, colnum, value, exact)
    o_diversity(object, ...)
    o_estimateR(object, ...)

Arguments

`object`	An OTUset or a TAXset object.
`colnum`	The column of the `sampleData` or `assignmentData` dataframe that contains the value.
`value`	The desired value.
`exact`	If exact=T `value` must match perfectly. If exact=F `value` will grep instead of match.
`...`	Other arguments. Often these are passed to `abundance`

Details

getOTUs Returns OTU names that match given values in the assignmentData dataframe.
getSamples Returns sample names that match given values in the sampleData dataframe.
o_diversity Wrapper for vegan's diversity function.
o_estimateR Wrapper for vegan's estimateR function.
otuseqplot Plots the samples acording to number of OTUs and number of sequences.
otusize Returns the size of each OTU.
otuspersample Lists the number of OTUs in each sample.
rseqplot Plots the samples by estimated richness and number of sequences.
seqspersample Returns the number of sequences in each sample.
sharedotus Returns the number of OTUs shared between samples.

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE)

o_estimateR(soginOTU)

## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE)

o_estimateR(soginOTU)

Other Generics

Description

Various functions. notus returns the number of OTUs in an OTUset object. nsamples returns the number of samples in either an OTUset or a TAXset object. seqnames returns the sequence names of the OTUset or TAXset object without the extra information commonly present with the id.

Usage

    notus(object, ...)
    nsamples(object, ...)
    seqnames(object, ...)
notus(object, ...)
    nsamples(object, ...)
    seqnames(object, ...)

Arguments

`object`	An OTUset or a TAXset object.
`...`	Other arguments. These are currently nonfunctional.

Examples


dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get the number of OTUs
notus(soginOTU)

## get the number of samples
nsamples(soginOTU)

dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get the number of OTUs
notus(soginOTU)

## get the number of samples
nsamples(soginOTU)

readOTUset

Description

This function reads in data and creates an OTUset object

Usage

    readOTUset(dirPath, otufile, level, fastafile, qualfile, samplefile, sampleADF, assignmentADF, sADF.names, aADF.names, rdp=F, otufiletype)
readOTUset(dirPath, otufile, level, fastafile, qualfile, samplefile, sampleADF, assignmentADF, sADF.names, aADF.names, rdp=F, otufiletype)

Arguments

`dirPath`	The directory path were the datafile are located. This is the current directory by default.
`otufile`	The OTU file. The only format currently supported is the Mothur format for .list files.
`level`	The OTU clustering level. By default this is 0.03. This level must correspond to levels present in the otufile.
`fastafile`	The fasta file. This is read in by ShortRead.
`qualfile`	The quality file. This is read in by ShortRead.
`samplefile`	The sample file. Currently this must be in Mothur format (.groups).
`sampleADF`	The sample meta data file. This is in AnnotatedDataFrame format.
`assignmentADF`	The assignment meta data file (the OTU meta data). This is generally in AnnotatedDataFrame format although it is also possible to read in an RDP classification file if there is only one read classification for each cluster and `rdp`=TRUE.
`sADF.names`	The column of the sampleADF file that has the sample names.
`aADF.names`	The column of the assignmentADF file that has the assignment names.
`rdp`	By default this is FALSE. Change to TRUE if assignmentADF is an RDP classification file. The RDP file must be in the fixed format.
`otufiletype`	The type of OTU file. Takes values "mothur", "cdhit", and "blastclust". Defaults to "mothur".

Examples


dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

soginOTU

dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

soginOTU

readTAXset

Description

Function to read in data and create a TAXset object

Usage

    readTAXset(dirPath, taxfile, namefile, fastafile, qualfile, samplefile, sampleADF, assignmentADF, sADF.names, aADF.names, type, ...)
readTAXset(dirPath, taxfile, namefile, fastafile, qualfile, samplefile, sampleADF, assignmentADF, sADF.names, aADF.names, type, ...)

Arguments

`dirPath`	The directory path were the datafile are located. This is the current directory by default.
`taxfile`	The classification file. The default format is RDP's fixed format.
`namefile`	A names file in the Mothur format. This is used to add removed unique sequences back into the dataset.
`fastafile`	The fasta file. This is read in by ShortRead.
`qualfile`	The quality file. This is read in by ShortRead.
`samplefile`	The sample file. Currently this must be in Mothur format (.groups).
`sampleADF`	The sample meta data file. This is in AnnotatedDataFrame format.
`assignmentADF`	The assignment meta data file (the OTU meta data) This is in AnnotatedDataFrame format.
`sADF.names`	The column of the sampleADF file that has the sample names.
`aADF.names`	The column of the assignmentADF file that has the assignment names.
`type`	This is the type of taxfile. By default this is the RDP fixed format. However, if `type` is changed to anything else the `read.table` function is used to read in the `taxfile`. In this case the first column of the taxfile must be the sequence names.
`...`	Additional arguments passed to `read.table` to read in the taxfile.

Examples


dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into TAXset object
soginTAX <- readTAXset(dirPath=dirPath, samplefile="sogin.groups", fastafile="sogin.fasta", taxfile="sogin.unique.fix.tax", namefile="sogin.names", sampleADF="sample_metadata.txt")

soginTAX

dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into TAXset object
soginTAX <- readTAXset(dirPath=dirPath, samplefile="sogin.groups", fastafile="sogin.fasta", taxfile="sogin.unique.fix.tax", namefile="sogin.names", sampleADF="sample_metadata.txt")

soginTAX

sampleData

Description

These functions access and replace the sampleData slot of OTUbase objects. sampleData and sampleData<- access and replace the AnnotatedDataFrame sampleData. sampleLabels and sampleLabels<- access and replace the labels of this AnnotatedDataFrame. sData and sData<- access and replace the dataframe component of the AnnotatedDataFrame.

Usage


    sData(object,...)
    sData(object)<-value
    sampleData(object,...)
    sampleData(object)<-value
    sampleLabels(object,...)
    sampleLabels(object)<-value

sData(object,...)
    sData(object)<-value
    sampleData(object,...)
    sampleData(object)<-value
    sampleLabels(object,...)
    sampleLabels(object)<-value

Arguments

`object`	An OTUset or a TAXset object
`value`	The replacement value for `sampleData` or `sampleLabels`
`...`	Added for completeness. Enables the passing of arguments.

Value

sData returns a dataframe. sampleData returns an AnnotatedDataFrame. sampleLabels returns a character. assignmentNames returns a character.

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get the sData dataframe
sData(soginOTU)

## get the sampleData slot
sampleData(soginOTU)

## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get the sData dataframe
sData(soginOTU)

## get the sampleData slot
sampleData(soginOTU)

subOTUset

Description

Function to get a subset of an OTUset object.

Usage


subOTUset(object, samples, otus)

subOTUset(object, samples, otus)

Arguments

`object`	An OTUset object
`samples`	A list of sample names
`otus`	A list of OTU names

Value

subOTUset returns an OTUset

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get subset of soginOTU

subOTUset(soginOTU, samples=getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE))

## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into OTUset object
soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt")

## get subset of soginOTU

subOTUset(soginOTU, samples=getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE))

subTAXset

Description

Function to get a subset of an TAXset object.

Usage


subTAXset(object, samples)

subTAXset(object, samples)

Arguments

`object`	An TAXset object
`samples`	A list of sample names

Value

subTAXset returns an TAXset

Examples


## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into TAXset object
soginTAX <- readTAXset(dirPath=dirPath, samplefile="sogin.groups", fastafile="sogin.fasta", taxfile="sogin.unique.fix.tax",namefile="sogin.names", sampleADF="sample_metadata.txt")

## get subset of soginTAX

subTAXset(soginTAX, samples=getSamples(soginTAX, colnum="Site", value="Labrador", exact=FALSE))

## locate directory with data
dirPath <- system.file("extdata/Sogin_2006", package="OTUbase")

## read in data into TAXset object
soginTAX <- readTAXset(dirPath=dirPath, samplefile="sogin.groups", fastafile="sogin.fasta", taxfile="sogin.unique.fix.tax",namefile="sogin.names", sampleADF="sample_metadata.txt")

## get subset of soginTAX

subTAXset(soginTAX, samples=getSamples(soginTAX, colnum="Site", value="Labrador", exact=FALSE))

Package 'OTUbase'

Help Index

The OTUbase package: A tool for organizing and manipulating Operational Taxonomic Unit data

Description

Details

Author(s)

References

"OTUset" class for OTU data

Description

Slots

Methods

Examples

"TAXset" class for TAX data

Description

Slots

Methods

Examples

abundance

Description

Usage

Arguments

Details

Value

Examples

Accessor functions for OTUset and TAXset objects

Description

Usage

Arguments

Value

See Also

Examples

assignmentData

Description

Usage

Arguments

Value

Examples

clusterSamples

Description

Usage

Arguments

Details

Examples

Other functions

Description

Usage

Arguments

Details

Examples

Other Generics

Description

Usage

Arguments

Examples

readOTUset

Description

Usage

Arguments

Examples

readTAXset

Description

Usage

Arguments

Examples

sampleData

Description

Usage

Arguments

Value

Examples

subOTUset

Description

Usage

Arguments

Value

Examples

subTAXset

Description

Usage

Arguments