tillingSet: This object contains an ExpressionSet

In rMAT: R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.

Description

This object contains an ExpressionSet and has the following additional slots: genomeName, featureSequence, featurePosition, featureChromosome, featureCopyNumber

Details

Tiling set objects can also be combined using the rbind methods. This is particularly useful when several arrays span a genome/chromosome.

Author(s)

Charles Cheung, [e-mail] and Raphael Gottardo, [e-mail] Arnaud Droit, [e-mail]

References

W. E. Johnson, Li, W., Meyer, C. A., Gottardo, R., Carroll, J. S., Brown, M., and Liu, X. S. (2006). Model-based analysis of tiling-arrays for ChIP-chip. PNAS 103:12457-12462.

See Also

BPMAPCelParser, NormalizeProbes

Examples

featureChromosome=factor(c("chr1","chr1","chr1","chr1"))
featurePosition=c(as.integer(47193),as.integer(47197),as.integer(47201),
    as.integer(47205))
featureCopyNumber=c(as.integer(1),as.integer(1),as.integer(1),as.integer(1))
a=5.379897
exprs=matrix(a,nrow=4)
genomeName="Sc03b_MR_v04_10000"
featureSequence=c("TCATCAAGGGAAGAGAGTCTCTCAG","TGATCATCACGGGACTTCTGGTTTA","CGGGACTTCTGGTTTATGGAACTAT","ACTTCTGGTTTATGGAACTATAAGG")

newSet <- new('tilingSet', featureChromosome=featureChromosome,
    featurePosition=featurePosition,featureCopyNumber=featureCopyNumber,
    exprs=exprs, genomeName=genomeName, featureSequence=featureSequence)

rMAT documentation built on May 6, 2019, 2:10 a.m.