tilingSet {rMAT}R Documentation

This object contains an ExpressionSet

Description

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

Usage

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

Arguments

tilingSet This object contains an ExpressionSet
genomeName String containing the genome name used (vector).
featureChromosome String containing the name of chromosome used (vector).
featurePosition String containing the Position of the sequences (vector).
featureCopyNumber String containing the copy number of sequence (vector).
exprs String containing the expresion data of enriched region (matrix with n column.
featureSequence String containing the sequence (vector).
experimentData String containing the type of experiments.

Author(s)

Charles Cheung, cykc@interchange.ubc.ca and Raphael Gottardo, raphael.gottardo@ircm.qc.ca Arnaud Droit, arnaud.droit@ircm.qc.ca

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

MAT

Examples


featureChromosome=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)


[Package rMAT version 1.1.2 Index]