beadarraySNP (version 1.38.0)

standardNormalization: Default complete normalization

Description

Performs all steps in normalization at best settings as determined in ref.

Usage

standardNormalization(snpdata)

Arguments

snpdata

SnpSetIllumina object with raw data

Value

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.

Details

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)

See Also

normalizeBetweenAlleles.SNP,normalizeWithinArrays.SNP, normalizeLoci.SNP

Examples

  data(chr17.260)
  data.nrm<-standardNormalization(chr17.260)