epi_preprocess: Preprocess methylation array

In isglobal-brge/EpiMutations: Robust outlier identification for DNA methylation data

Preprocess methylation array

Description

The epi_preprocess function reads Illumina methylation sample sheet for case samples and it merges them with RGChannelSet reference panel. The final dataset is normalized using minfi package preprocess methods.

Usage

epi_preprocess(
  cases_dir,
  reference_panel,
  pattern = "csv$",
  normalize = "raw",
  norm_param = norm_parameters(),
  verbose = FALSE
)

Arguments

cases_dir	the base directory from which the search is started.
reference_panel	an RGChannelSet object containing the reference panel (controls) samples.
pattern	What pattern is used to identify a sample sheet file.
normalize	a character string specifying the selected preprocess method. For more information see Details or minfi package user's Guide. It can be set as: "raw", "illumina", "swan", "quantile", "noob" or "funnorm".)
norm_param	the parameters for each preprocessing method. See the function norm_parameters.
verbose	logical. If TRUE additional details about the procedure will provide to the user. The default is FALSE.

Details

The epi_preprocess function reads Illumina methylation sample sheet for case samples and it merges them with RGChannelSet reference panel. The final dataset is normalized using different minfi package preprocess methods:

• "raw": preprocessRaw

• "illumina": preprocessIllumina

• "swan": preprocessSWAN

• "quantile": preprocessQuantile

• "noob": preprocessNoob

• "funnorm": preprocessFunnorm

Value

epi_preprocess function returns a GenomicRatioSet object containing case and control (reference panel) samples.

Examples

# The reference panel for this example is available in 
#epimutacionsData (ExperimentHub) package

   library(ExperimentHub)
   eh <- ExperimentHub()
   query(eh, c("epimutacionsData"))
   reference_panel <- eh[["EH6691"]]
   cases_dir <- system.file("extdata", package = "epimutacionsData")
   #Preprocessing

   epi_preprocess( cases_dir, 
                   reference_panel, 
                   pattern = "SampleSheet.csv")

isglobal-brge/EpiMutations documentation built on April 20, 2024, 9:05 a.m.