beadarraySNP (version 1.38.0)

normalizeLoci.SNP: locus normalization

Description

Perform locus normalization on Illumina Golden Gate bead arrays

Usage

normalizeLoci.SNP(object, method=c("normals","paired","alleles"), 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. "alleles" fits a linear model between the B-allele ratio and the signal intensity and normalizes for that

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

Value

This function returns an SnpSetIllumina object.

Details

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

See Also

SnpSetIllumina,normalizeWithinArrays.SNP, normalizeBetweenAlleles.SNP

Examples

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