standardNormalization {beadarraySNP} | R Documentation |
Performs all steps in normalization at best settings as determined in ref.
standardNormalization(snpdata)
snpdata |
SnpSetIllumina object with raw data |
The function performs in the following steps
snpdata<-normalizeBetweenAlleles.SNP(snpdata)
snpdata<-normalizeWithinArrays.SNP(snpdata,callscore = 0.8, relative = TRUE,
fixed = FALSE, quantilepersample = TRUE)
snpdata<-normalizeLoci.SNP(snpdata,normalizeTo = 2)
A SnpSetIllumina
object with the G, R and intensity
elements in
assayData normalized to obtain values close to 2 on a linear scale for
unaffected material.
Jan Oosting
normalizeBetweenAlleles.SNP
,normalizeWithinArrays.SNP
,
normalizeLoci.SNP
data(chr17.260) data.nrm<-standardNormalization(chr17.260)