normalizeLoci.SNP: locus normalization

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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

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)

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.