"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")

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/OTUset-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: .OTUset-class
> ### Title: "OTUset" class for OTU data
> ### Aliases: OTUset OTUsetB-class OTUsetF-class OTUsetQ-class OTUsetB
> ###   OTUsetF OTUsetQ
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass(".OTUset")
Class ".OTUset" [package "OTUbase"]

Slots:
                                                               
Name:               otuID           sampleID     assignmentData
Class:          character          character AnnotatedDataFrame
                         
Name:          sampleData
Class: AnnotatedDataFrame

Extends: ".OTUbase"

Known Subclasses: "OTUsetF", "OTUsetQ", "OTUsetB"
> showMethods(class=".OTUset")

Function "%&%":
 <not an S4 generic function>

Function ".RsamtoolsFileList":
 <not an S4 generic function>

Function ".ShortReadFile":
 <not an S4 generic function>

Function ".asSpace":
 <not an S4 generic function>

Function ".bowtie_mismatches":
 <not an S4 generic function>

Function ".clone":
 <not an S4 generic function>

Function ".filter":
 <not an S4 generic function>

Function ".replaceSEW":
 <not an S4 generic function>

Function ".report_pdf":
 <not an S4 generic function>

Function ".srValidity":
 <not an S4 generic function>

Function ".throw":
 <not an S4 generic function>

Function ".validity":
 <not an S4 generic function>

Function "BunchKaufman":
 <not an S4 generic function>

Function "Cholesky":
 <not an S4 generic function>

Function "Schur":
 <not an S4 generic function>

Function "XString":
 <not an S4 generic function>

Function "XStringSet":
 <not an S4 generic function>
Function: abundance (package OTUbase)
object=".OTUset"


Function "all.equal":
 <not an S4 generic function>

Function "as.array":
 <not an S4 generic function>

Function "band":
 <not an S4 generic function>

Function "chol":
 <not an S4 generic function>

Function "chol2inv":
 <not an S4 generic function>

Function "clone":
 <not an S4 generic function>
Function: clusterSamples (package OTUbase)
object=".OTUset"


Function "commonColnames":
 <not an S4 generic function>

Function "compatibleStrand":
 <not an S4 generic function>

Function "constraint":
 <not an S4 generic function>

Function "constraint<-":
 <not an S4 generic function>

Function "cov2cor":
 <not an S4 generic function>

Function "crossprod":
 <not an S4 generic function>

Function "decode":
 <not an S4 generic function>

Function "determinant":
 <not an S4 generic function>

Function "diag":
 <not an S4 generic function>

Function "diag<-":
 <not an S4 generic function>

Function "dups":
 <not an S4 generic function>

Function "expm":
 <not an S4 generic function>

Function "extraColumnSlotNames":
 <not an S4 generic function>

Function "facmul":
 <not an S4 generic function>

Function "forceSymmetric":
 <not an S4 generic function>

Function "format":
 <not an S4 generic function>

Function "isDiagonal":
 <not an S4 generic function>

Function "isSymmetric":
 <not an S4 generic function>

Function "isTriangular":
 <not an S4 generic function>

Function "loadSequence":
 <not an S4 generic function>

Function "ls":
 <not an S4 generic function>

Function "lu":
 <not an S4 generic function>

Function "maxQuality":
 <not an S4 generic function>

Function "minQuality":
 <not an S4 generic function>

Function "nnzero":
 <not an S4 generic function>

Function "norm":
 <not an S4 generic function>
Function: notus (package OTUbase)
object=".OTUset"


Function "offset":
 <not an S4 generic function>

Function "orderAsRanges":
 <not an S4 generic function>
Function: otuID (package OTUbase)
object=".OTUset"


Function "p2q":
 <not an S4 generic function>

Function "pack":
 <not an S4 generic function>

Function "print":
 <not an S4 generic function>

Function "process_self_hits":
 <not an S4 generic function>

Function "q2p":
 <not an S4 generic function>

Function "qr":
 <not an S4 generic function>

Function "qr.Q":
 <not an S4 generic function>

Function "qr.R":
 <not an S4 generic function>

Function "qr.coef":
 <not an S4 generic function>

Function "qr.fitted":
 <not an S4 generic function>

Function "qr.qty":
 <not an S4 generic function>

Function "qr.qy":
 <not an S4 generic function>

Function "qr.resid":
 <not an S4 generic function>

Function "rcond":
 <not an S4 generic function>

Function "selectSomeIndex":
 <not an S4 generic function>
Function: show (package methods)
object=".OTUset"


Function "skewpart":
 <not an S4 generic function>

Function "solve":
 <not an S4 generic function>

Function "symmpart":
 <not an S4 generic function>

Function "tcrossprod":
 <not an S4 generic function>

Function "toeplitz":
 <not an S4 generic function>

Function "tril":
 <not an S4 generic function>

Function "triu":
 <not an S4 generic function>

Function "twoWayAlphabetFrequencyByQuality":
 <not an S4 generic function>

Function "unname":
 <not an S4 generic function>

Function "unpack":
 <not an S4 generic function>

Function "updateCigarAndStart":
 <not an S4 generic function>

Function "updown":
 <not an S4 generic function>

Function "upperBound":
 <not an S4 generic function>

Function "upperBoundIsStrict":
 <not an S4 generic function>

Function "writeMM":
 <not an S4 generic function>

Function "zapsmall":
 <not an S4 generic function>
> showClass("OTUsetQ")
Class "OTUsetQ" [package "OTUbase"]

Slots:
                                                               
Name:             quality              sread                 id
Class:       QualityScore       DNAStringSet         BStringSet
                                                               
Name:               otuID           sampleID     assignmentData
Class:          character          character AnnotatedDataFrame
                         
Name:          sampleData
Class: AnnotatedDataFrame

Extends: 
Class "ShortReadQ", directly
Class ".OTUset", directly
Class "ShortRead", by class "ShortReadQ", distance 2
Class ".OTUbase", by class ".OTUset", distance 2
Class ".ShortReadBase", by class "ShortReadQ", distance 3
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>