getNormInd: Retrieve sub-bead pool indexes

In beadarrayMSV: Analysis of Illumina BeadArray SNP data including MSV markers

Description

Creates an array of logical indexes to each bead-type for use in normalization

Usage

getNormInd(beadInfo, featureNames, normID = NULL, verbose = TRUE)

Arguments

beadInfo	Data-frame containg data on each marker in the experiment, specifically the “Address”, “Address2”, and “Norm.ID” connecting beads to markers (usually exported from Illumina's GenomeStudio Genotyping Module)
featureNames	Character vector with bead-type names (addresses)
normID	Character vector with one or more sub-bead pool indexes. If NULL, all Norm.ID's found in beadInfo are used
verbose	If TRUE, the sum of each sub-bead pool is printed

Value

Matrix of size (length(featureNames) x length(normID)), with logical indices to the sub-bead pool to which each bead-type belongs

Note

Beads manufactured in different pools should be normalised separately

Author(s)

Lars Gidskehaug

See Also

preprocessBeadSet, getNoiseDistributions

Examples

## Not run: 
#Common use includes BeadSetIllumina-object
rPath <- system.file("extdata", package="beadarrayMSV")
BSDataRaw <- readBeadSummaryOutput(path=rPath,recursive=TRUE)
beadInfo <- read.table(paste(rPath,'beadData.txt',sep='/'),sep='\t',
    header=TRUE,as.is=TRUE)
rownames(beadInfo) <- make.names(beadInfo$Name)
normInd <- getNormInd(beadInfo,featureNames(BSDataRaw))

## End(Not run)

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

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

Loading required package: geneplotter
Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
R session is headless; GTK+ not initialized.
Found 4 arrays
Sum Norm.IDs:
   2  102  202    1  201  101 
2347  562  358  170   56   80 

beadarrayMSV documentation built on May 1, 2019, 6:33 p.m.