Storage of annotation information

Description

An interface to set or retrieve information about the annotation of a beadLevelData or ExpressionSetIllumina object.

Usage

    suggestAnnotation(data,verbose=FALSE)
    annotation(object,...)

Arguments

.

Details

A character string is used to specify the annotation with the currently supported values being; Humanv4, Humanv3, Humanv2, Humanv1, Mousev2, Mousev1, Mousev1p1 and Ratv1. This string is used within beadarray to retrieve control probe IDs within particular QC functions.

The suggestAnnotation function tries to determine a suitable value for a beadLevelData-class based on the probe IDs and compiled list of IDs from all expression platforms. This is based on the percentage of IDs on the array that overlap with IDs from known platforms. The platform with highest overlap is chosen.

Author(s)

Mark Dunning

Examples

if(require(beadarrayExampleData)){

data(exampleBLData)

annotation(exampleBLData)

suggestAnnotation(exampleBLData,verbose=TRUE)

annotation(exampleBLData) <- "Humanv2"
 

data(exampleSummaryData)

annotation(exampleSummaryData)

annotation(exampleBLData) <- "Humanv1"

}

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(beadarray)
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: 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: ggplot2
Welcome to beadarray version 2.22.2
beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/beadarray/annotationInterface.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Annotation
> ### Title: Storage of annotation information
> ### Aliases: annotation,beadLevelData-method
> ###   annotation,ExpressionSetIllumina-method
> ###   annotation<-,beadLevelData,character-method
> ###   annotation<-,ExpressionSetIllumina,character-method annotation
> ###   getControlProfile suggestAnnotation
> 
> ### ** Examples
> 
> 
> if(require(beadarrayExampleData)){
+ 
+ data(exampleBLData)
+ 
+ annotation(exampleBLData)
+ 
+ suggestAnnotation(exampleBLData,verbose=TRUE)
+ 
+ annotation(exampleBLData) <- "Humanv2"
+  
+ 
+ data(exampleSummaryData)
+ 
+ annotation(exampleSummaryData)
+ 
+ annotation(exampleBLData) <- "Humanv1"
+ 
+ }
Loading required package: beadarrayExampleData
Percentage of overlap with IDs on this array and known expression platforms
HUMANREF8_V3_0_R1_11282963_A_WGDASL        HumanHT12_V3_0_R3_11283641_A 
                           48.78621                            97.16521 
       HumanHT12_V4_0_R1_15002873_B        HumanHT12_V4_0_R2_15002873_B 
                           83.70782                            84.05715 
HumanHT12_V4_0_R2_15002873_B_WGDASL                        HumanRef8_V1 
                           54.68237                            37.33872 
       HumanRef8_V2_0_R2_11223162_A        HumanRef8_V2_0_R4_11223162_A 
                           38.88553                            38.88470 
       HumanRef8_V3_0_R0_11282963_A        HumanRef8_V3_0_R3_11282963_A 
                           48.78621                            48.78621 
                        HumanWG6_V1         HumanWG6_V2_0_R2_11223189_A 
                           37.33872                            81.32701 
        HumanWG6_V2_0_R4_11223189_A              HumanWG6_V2_11223189_B 
                           81.32619                            81.32619 
        HumanWG6_V3_0_R3_11282955_A                        MouseRef8_V1 
                           97.16521                            36.67984 
       MouseRef8_V1_1_R4_11234312_A        MouseRef8_V2_0_R3_11278551_A 
                           38.10629                            43.77615 
                        MouseWG6_V1         MouseWG6_V1_1_R4_11234304_A 
                           36.67984                            38.10629 
                      MouseWG6_V1_B         MouseWG6_V2_0_R3_11278593_A 
                           36.58768                            78.45060 
        RatRef12_V1_0_R5_11222119_A 
                           36.06644 
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>