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,...)

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)

Results

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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/assignmentData.Rd_%03d_medium.png", width=480, height=480)
> ### Name: assignmentData
> ### Title: assignmentData
> ### Aliases: aData aData,.OTUbase-method aData<- aData<-,.OTUbase-method
> ###   aData<-,.OTUbase,data.frame-method assignmentData
> ###   assignmentData,.OTUbase-method assignmentData<-
> ###   assignmentData<-,.OTUbase-method
> ###   assignmentData<-,.OTUbase,AnnotatedDataFrame-method assignmentLabels
> ###   assignmentLabels,.OTUbase-method assignmentLabels<-
> ###   assignmentLabels<-,.OTUbase-method
> ###   assignmentLabels<-,.OTUbase,character-method
> ###   assignmentNames,.OTUbase-method assignmentNames
> 
> ### ** 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
> 
> ## get the aData dataframe
> aData(soginOTU)
data frame with 0 columns and 0 rows
> 
> ## get the assignmentData slot
> assignmentData(soginOTU)
An object of class 'AnnotatedDataFrame': none
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>