normalize450K: Preprocessing of Illumina Infinium 450K data

Share:

Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K '.idat' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.

Author
Jonathan Alexander Heiss
Date of publication
None
Maintainer
Jonathan Alexander Heiss <jonathan.heiss@posteo.de>
License
BSD_2_clause + file LICENSE
Version
1.2.0

View on Bioconductor

Man pages

estimateLC
Estimation of Leukocyte composition for whole blood samples
read_and_normalize450K
Normalization of 450K data by LOESS method

Files in this package

normalize450K/DESCRIPTION
normalize450K/LICENSE
normalize450K/NAMESPACE
normalize450K/R
normalize450K/R/estimateLC.R
normalize450K/R/read_and_normalize450K.R
normalize450K/R/sysdata.rda
normalize450K/build
normalize450K/build/vignette.rds
normalize450K/inst
normalize450K/inst/CITATION
normalize450K/inst/doc
normalize450K/inst/doc/read_and_normalize450K.R
normalize450K/inst/doc/read_and_normalize450K.Rnw
normalize450K/inst/doc/read_and_normalize450K.pdf
normalize450K/man
normalize450K/man/estimateLC.Rd
normalize450K/man/read_and_normalize450K.Rd
normalize450K/vignettes
normalize450K/vignettes/per_sample_correlation_beta.png
normalize450K/vignettes/per_sample_correlation_rank.png
normalize450K/vignettes/read_and_normalize450K.Rnw