rnb.execute.normalization {RnBeads} | R Documentation |
Performs normalization of the provided HumanMethylation450 data set.
rnb.execute.normalization( object, method = rnb.getOption("normalization.method"), bgcorr.method = rnb.getOption("normalization.background.method"), verbose = TRUE )
object |
Methylation dataset as an object of type |
method |
Normalization method, must be one of |
bgcorr.method |
Character singleton specifying which background subtraction should be used. Only methods impemented
in the methylumi package are supported at the moment, namely |
verbose |
flag specifying whether diagnostic output should be written to the console or to the RnBeads logger in case the latter is initialized |
Normalized dataset as an object of type RnBeadSet
.
Pavlo Lutsik
1. Triche, Timothy J., Jr., Weisenberger, Daniel J., Van Den Berg, David, Laird, Peter W. and Siegmund, Kimberly D. (2013) Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Research 41(7):e90-e90.
library(RnBeads.hg19) data(small.example.object) logger.start(fname=NA) rnb.set.norm<-rnb.execute.normalization(rnb.set.example, method="illumina", bgcorr.method="none")