meffonym.bmiq.calibration: BMIQ normalization to a standard
In perishky/meffonym: DNA methylation exposure and phenotypic archive
meffonym.bmiq.calibration R Documentation
BMIQ normalization to a standard
Description
Methylation levels are normalized so that they are comparable to a given dataset. It is based on
BMIQ:
Usage
meffonym.bmiq.calibration(x, standard, ...)
Arguments
x
DNA methylation matrix (rows=CpG sites, columns=samples).
standard
A named vector of methylation levels corresponding to the row names of x.
...
See http://code.google.com/p/bmiq/ for more details.
Details
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.
Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S.
Bioinformatics. 2013 Jan 15;29(2):189-96. doi: 10.1093/bioinformatics/bts680. Epub 2012 Nov 21.
PMID: 23175756
The code was obtained from http://labs.genetics.ucla.edu/horvath/dnamage/NORMALIZATION.R.
Value
Matrix identical to x but with methylation levels normalized
by BMIQ to the standard and rows corresponding to standard.
Missing values in x are imputed by k-nearest neighbor.
perishky/meffonym documentation built on Nov. 8, 2024, 8:36 p.m.
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| meffonym.bmiq.calibration | R Documentation |
BMIQ normalization to a standard
Description
Methylation levels are normalized so that they are comparable to a given dataset. It is based on BMIQ:
Usage
meffonym.bmiq.calibration(x, standard, ...)
Arguments
x |
DNA methylation matrix (rows=CpG sites, columns=samples). |
standard |
A named vector of methylation levels corresponding to the row names of |
... |
See http://code.google.com/p/bmiq/ for more details. |
Details
A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Teschendorff AE, Marabita F, Lechner M, Bartlett T, Tegner J, Gomez-Cabrero D, Beck S. Bioinformatics. 2013 Jan 15;29(2):189-96. doi: 10.1093/bioinformatics/bts680. Epub 2012 Nov 21. PMID: 23175756
The code was obtained from http://labs.genetics.ucla.edu/horvath/dnamage/NORMALIZATION.R.
Value
Matrix identical to x but with methylation levels normalized
by BMIQ to the standard and rows corresponding to standard.
Missing values in x are imputed by k-nearest neighbor.
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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