Class "MapFilterProbe"

Description

class to store probe information after remapping and/or filtering of probes.

Usage

## Accessors

getChromosome(object)
getFilteredIndices(object)
getPosition(object)
getStrand(object)

Arguments

Objects from the Class

Objects can be created by calls of the form new("mapFilterProbe", filteredIndices, chromosome, position, strand).

Slots

filteredIndices:

Object of class "vector" ~~

chromosome:

Object of class "vector" ~~

position:

Object of class "vector" ~~

strand:

Object of class "vector" ~~

Methods

getChromosome

signature(object = "MapFilterProbe"): ...

getFilteredIndices

signature(object = "MapFilterProbe"): ...

getPosition

signature(object = "MapFilterProbe"): ...

getStrand

signature(object = "MapFilterProbe"): ...

initialize

signature(.Object = "MapFilterProbe"): ...

selectProbesFromFilterOverlap

signature(object = "MapFilterProbe"): ...

show

signature(object = "MapFilterProbe"): ...

Accessors

In the following code snippets, x is a MapFilterProbe object.

getChromosome(x): Extract the chromosome identifiers.

getFilteredIndices(x): Extract the filtered probe indices.

getPosition(x): Extract the genomic position of the filtered probes.

getStrand(x): Extract the strand orientation info for the filtered probes.

Author(s)

Kristof De Beuf <kristof.debeuf@ugent.be>

Examples

  showClass("MapFilterProbe")
  
  library(waveTilingData)
  data(leafdevMapAndFilterTAIR9)
  tt1 <- getChromosome(leafdevMapAndFilterTAIR9)
  tt2 <- getFilteredIndices(leafdevMapAndFilterTAIR9)
  tt3 <- getPosition(leafdevMapAndFilterTAIR9)
  tt4 <- getStrand(leafdevMapAndFilterTAIR9)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(waveTiling)
Loading required package: oligo
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

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
Loading required package: GenomeGraphs
Loading required package: biomaRt
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/waveTiling/MapFilterProbe-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MapFilterProbe-class
> ### Title: Class "MapFilterProbe"
> ### Aliases: MapFilterProbe-class MapFilterProbe
> ###   getChromosome,MapFilterProbe-method getChromosome
> ###   getFilteredIndices,MapFilterProbe-method getFilteredIndices
> ###   getPosition,MapFilterProbe-method getPosition
> ###   getStrand,MapFilterProbe-method getStrand
> ###   initialize,MapFilterProbe-method
> ###   selectProbesFromFilterOverlap,MapFilterProbe-method
> ###   show,MapFilterProbe-method
> ### Keywords: classes
> 
> ### ** Examples
> 
>   showClass("MapFilterProbe")
Class "MapFilterProbe" [package "waveTiling"]

Slots:
                                                                      
Name:  filteredIndices      chromosome        position          strand
Class:          vector          vector          vector          vector
>   
>   library(waveTilingData)
>   data(leafdevMapAndFilterTAIR9)
>   tt1 <- getChromosome(leafdevMapAndFilterTAIR9)
>   tt2 <- getFilteredIndices(leafdevMapAndFilterTAIR9)
>   tt3 <- getPosition(leafdevMapAndFilterTAIR9)
>   tt4 <- getStrand(leafdevMapAndFilterTAIR9)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>