Functions for preprocessing

Functions for preprocessing

Convert fluorescence intensities to beta-values

Usage

correct_dye_bias(raw)

correct_dye_bias2(raw)

beta_values(raw)

Arguments

raw

Output of calling read_idats

Value

A modified raw object with dye-bias corrected intensities using RELIC for correct_dye_bias. A matrix of beta-values, either normalized (for normalize) or not (for dont_normalize).

A matrix of beta-values. If IDATs were imported with option on_disk = TRUE, a {codeff object. If the data was imported using on_disk = TRUE, it is recommended to transpose the returned ff object for fast row-based access.

References

Xu Z, Langie SA, De Boever P, Taylor JA, Niu L. RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip. BMC Genomics. 2017 Jan 3;18(1):4.

Heiss JA, Brenner H. Between-array normalization for 450K data. Frontiers in Genetics. 2015;6.

Author

Jonathan Heiss