normalizeLoci.SNP {beadarraySNP}R Documentation

locus normalization

Description

Perform locus normalization on Illumina Golden Gate bead arrays

Usage

   normalizeLoci.SNP(object, method=c("normals","paired"), NorTum="NorTum",
                     Gender="Gender", Subject="Subject", normalizeTo=2, trig=FALSE)

Arguments

object object class SnpSetIllumina
method character. If "normals" then all normal samples in the dataset are used as the invariant set. If "paired" then affected samples are normalized to their paired normal samples
NorTum logical or character vector or name of column in pData slot. depicts the normal, unaffected samples in the dataset. In a character vector these should have the value "N"
Gender logical or character vector or name of column in pData slot. depicts the female samples in the dataset and is used to normalize the sex chromosomes. In a character vector these should have value "F"
Subject factor or name of or column in pData slot. This factor is used to pair the samples when method is "paired"
normalizeTo normalizeTo numeric. The average copy number of the sample.
trig Logical, use geometric distance of intensity. Otherwise use addition of intensities

Details

This function is usually performed in the last step of normalization in order to obtain calculated copy numbers.

Value

This function returns an SnpSetIllumina object.

Author(s)

Jan Oosting

See Also

SnpSetIllumina,normalizeWithinArrays.SNP, normalizeBetweenAlleles.SNP

Examples

  data(chr17.260)
  data.nrm<-normalizeLoci.SNP(chr17.260)


[Package beadarraySNP version 1.6.0 Index]