Polar transformations

Description

Perform polar transforms on Illumina Golden Gate bead arrays

Usage

   RG2polar(object,trig=FALSE)
   polar2RG(object,trig=FALSE)

Arguments

Details

RG2polar transforms the R and G matrices to theta and intensity matrices. Note that the intensity value is the sum of R and G and not the geometric distance to the origin.

polar2RG performs the reverse transformation

Value

This function returns an SnpSetIllumina object.

Author(s)

Jan Oosting

See Also

SnpSetIllumina-class

Examples

  data(chr17.260)
  data.polar<-RG2polar(chr17.260)
  plot(assayData(data.polar)$theta,assayData(data.polar)$intensity)

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 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(beadarraySNP)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: quantsmooth
Loading required package: quantreg
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarraySNP/PolarTransforms.Rd_%03d_medium.png", width=480, height=480)
> ### Name: PolarTransforms
> ### Title: Polar transformations
> ### Aliases: RG2polar polar2RG
> ### Keywords: manip
> 
> ### ** Examples
> 
>   data(chr17.260)
>   data.polar<-RG2polar(chr17.260)
>   plot(assayData(data.polar)$theta,assayData(data.polar)$intensity)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>