tilingSet {rMAT} | R Documentation |
This object contains an ExpressionSet and has the following additional slots: genomeName, featureSequence, featurePosition, featureChromosome, featureCopyNumber
newSet<-new('tilingSet', featureChromosome,featurePosition, featureCopyNumber, exprs, genomeName, featureSequence, experimentData)
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. |
Charles Cheung, cykc@interchange.ubc.ca and Raphael Gottardo, raphael.gottardo@ircm.qc.ca Arnaud Droit, arnaud.droit@ircm.qc.ca
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.
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)