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, ...)

Arguments

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> 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/other_generics.Rd_%03d_medium.png", width=480, height=480)
> ### Name: otherGenerics
> ### Title: Other Generics
> ### Aliases: notus notus,.OTUset-method nsamples nsamples,.OTUbase-method
> ###   seqnames seqnames,.OTUbase-method
> 
> ### ** 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")
Looking for column with names
> 
> ## get the number of OTUs
> notus(soginOTU)
[1] 399
> 
> ## get the number of samples
> nsamples(soginOTU)
[1] 8
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>