standardNormalization: Default complete normalization
In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
View source: R/SnpSetIlluminaNormalize.R
Description
Performs all steps in normalization at best settings as determined in ref.
Usage
1
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
1
2
data(chr17.260)
data.nrm<-standardNormalization(chr17.260)
beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/SnpSetIlluminaNormalize.R
Description
Performs all steps in normalization at best settings as determined in ref.
Usage
1 | 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
1 2 | data(chr17.260)
data.nrm<-standardNormalization(chr17.260)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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