dasen-exprmethy450: Calculate normalized betas from exprmethy450 of Illumina 450K...
In schalkwyk/wateRmelon: Illumina 450 and EPIC methylation array normalization and metrics
betaqn-exprmethy450-methods R Documentation
Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays
Description
Quantile normalize betas from exprmethy450 objects
Arguments
bn
An exprmethy450 object.
fudge
value added to total intensity to prevent denominators close to zero when
calculating betas
Details
betaqn quantile normalizes betas
Value
exprmethy450 object of the same shape and order as bn.
Author(s)
Leonard.Schalkwyk@kcl.ac.uk
References
[1] Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC:
A data-driven approach to preprocessing Illumina 450K methylation
array data (submitted)
[2] Dedeurwaerder S, Defrance M, Calonne E, Sotiriou C, Fuks F:
Evaluation of the Infinium Methylation 450K technology . Epigenetics
2011, 3(6):771-784.
[3] Touleimat N, Tost J: Complete pipeline for Infinium R Human
Methylation 450K BeadChip data processing using subset quantile
normalization for accurate DNA methylation estimation. Epigenomics
2012, 4:325-341
[4] Maksimovic J, Gordon L, Oshlack A: SWAN: Subset quantile
Within-Array Normalization for Illumina Infinium HumanMethylation450
BeadChips. Genome biology 2012, 13(6):R44
schalkwyk/wateRmelon documentation built on April 15, 2024, 12:06 p.m.
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| betaqn-exprmethy450-methods | R Documentation |
Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays
Description
Quantile normalize betas from exprmethy450 objects
Arguments
bn |
An exprmethy450 object. |
fudge |
value added to total intensity to prevent denominators close to zero when calculating betas |
Details
betaqn quantile normalizes betas
Value
exprmethy450 object of the same shape and order as bn.
Author(s)
Leonard.Schalkwyk@kcl.ac.uk
References
[1] Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach to preprocessing Illumina 450K methylation array data (submitted)
[2] Dedeurwaerder S, Defrance M, Calonne E, Sotiriou C, Fuks F: Evaluation of the Infinium Methylation 450K technology . Epigenetics 2011, 3(6):771-784.
[3] Touleimat N, Tost J: Complete pipeline for Infinium R Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics 2012, 4:325-341
[4] Maksimovic J, Gordon L, Oshlack A: SWAN: Subset quantile Within-Array Normalization for Illumina Infinium HumanMethylation450 BeadChips. Genome biology 2012, 13(6):R44
R Package Documentation
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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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