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, ...)

Arguments

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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OTUbase)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-0
================================================================================
Welcome to OTUbase version 1.22.0

Attaching package: 'OTUbase'

The following object is masked from 'package:GenomicAlignments':

    seqnames

The following object is masked from 'package:SummarizedExperiment':

    seqnames

The following object is masked from 'package:GenomicRanges':

    seqnames

The following object is masked from 'package:GenomeInfoDb':

    seqnames

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/OTUbase/clusterSamples.Rd_%03d_medium.png", width=480, height=480)
> ### Name: clusterSamples
> ### Title: clusterSamples
> ### Aliases: clusterSamples-generic clusterSamples-method
> ###   clusterSamples,.OTUset-method clusterSamples,.TAXset-method
> ###   clusterSamples
> 
> ### ** 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")
Looking for column with names
> 
> ## cluster samples
> clusterSamples(soginOTU, collab="Site", distmethod="jaccard")

Call:
hclust(d = d, method = clustermethod)

Cluster method   : complete 
Distance         : jaccard 
Number of objects: 8 

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>