Description Usage Arguments Value Note Author(s) See Also Examples
Creates an array of logical indexes to each bead-type for use in normalization
1 | getNormInd(beadInfo, featureNames, normID = NULL, verbose = TRUE)
|
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
|
verbose |
If |
Matrix of size (length(featureNames)
x length(normID)
),
with logical indices to the sub-bead pool to which each bead-type belongs
Beads manufactured in different pools should be normalised separately
Lars Gidskehaug
preprocessBeadSet
, getNoiseDistributions
1 2 3 4 5 6 7 8 9 10 | ## 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)
|
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
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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
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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
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