sigaR (version 1.18.0)

ExpressionSet2weightedSubset: Weighted subsetting ExpressionSet-objects.

Description

Limit an ExpressionSet object to a subset of its features, using weighted averaging of the expression signal.

Usage

ExpressionSet2weightedSubset(GEdata, featuresAndWeights, chr, 
bpstart, bpend, ncpus = 1, verbose=TRUE)

Arguments

GEdata

Object of class ExpressionSet.

featuresAndWeights

Object of class list. Each list item is a matrix. The first column of this matrix contains the row numbers of features to be maintained in the ExpressionSet-object. The second column contains the weights of each features, to be used in the calculation of the weighted average gene expression signal.

chr

Column in the slot featureData of the ExpressionSet-object specifying the chromosome information of the features.

bpstart

Column in the slot featureData of the ExpressionSet-object specifying the start basepair information of the features.

bpend

Column in the slot featureData of the ExpressionSet-object specifying the end basepair information of the features.

ncpus

Number of cpus to be used in computations.

verbose

Logical indicator: should intermediate output be printed on the screen?

Value

ExpressionSet, restricted to the specified subset of features.

Warning

The phenoData, experimentData, and other slots of the ExpressionSet-object are currently not passed on to the subsetted object.

Details

Annotation information of features with multiplicity larger than one is compressed as follows. It is assumed that all features map to the same chromosome, leaving no ambiguity. The start base pair of the "new" feature is the smallest start base pair of features from which it has been formed. The end base pair of the "new" feature is the largest end base pair of features from which it has been formed.

References

Van Wieringen, W.N., Unger, K., Leday, G.G.R., Krijgsman, O., De Menezes, R.X., Ylstra, B., Van de Wiel, M.A. (2012), "Matching of array CGH and gene expression microarray features for the purpose of integrative analysis", BMC Bioinformatics, 13:80.

See Also

ExpressionSet2subset

Examples

# load data
data(pollackGE16)

# extract genomic information from ExpressionSet-object
chr <- fData(pollackGE16)[,1]
bpstart <- fData(pollackGE16)[,2]
bpend <- fData(pollackGE16)[,3]

# find unique genomic locations
uniqInfo <- uniqGenomicInfo(chr, bpstart, bpend, verbose = FALSE) 

# subset ExpressionSet-object to features with unique genomic locations
pollackGE16 <- ExpressionSet2weightedSubset(pollackGE16, uniqInfo, 1, 2, 3)