standardNormalization {beadarraySNP}R Documentation

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

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)

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.

Author(s)

Jan Oosting

See Also

normalizeBetweenAlleles.SNP,normalizeWithinArrays.SNP, normalizeLoci.SNP

Examples

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

[Package beadarraySNP version 1.8.0 Index]