normalizeLoci.SNP {beadarraySNP} | R Documentation |
Perform locus normalization on Illumina Golden Gate bead arrays
normalizeLoci.SNP(object, method=c("normals","paired"), NorTum="NorTum", Gender="Gender", Subject="Subject", normalizeTo=2, trig=FALSE)
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 |
This function is usually performed in the last step of normalization in order to obtain calculated copy numbers.
This function returns an SnpSetIllumina
object.
Jan Oosting
SnpSetIllumina
,normalizeWithinArrays.SNP
,
normalizeBetweenAlleles.SNP
data(chr17.260) data.nrm<-normalizeLoci.SNP(chr17.260)