summarize: summarization of Illumina Human DNA Methylation array data

In bbmri-nl/MethylAid: Visual and interactive quality control of large Illumina DNA Methylation array data sets

Description

summarize is the main function when called all samples in the targets file will be summarized

Usage

summarize(targets, batchSize = -1, BPPARAM = NULL, rp.zero = TRUE,
  verbose = TRUE, file = NULL, ...)

Arguments

targets	valid minfi targets file
batchSize	the size of each the batch
BPPARAM	see bpparam()
rp.zero	Default TRUE replaces zero intensity values with NA's
verbose	default is TRUE
file	if given summarized data is stored as RData object
...	optional arguments to read.metharray.exp, i.e. force=TRUE

Details

By default the summarization is performed on all data at once. Optionally the data can be summarized in batches using the batchSize option. Summarization of data can be performed in parallel as well see the MethylAid vignette for examples.

Value

summarized data is saved optionally returned

Author(s)

mvaniterson

Examples

library(minfiData)
baseDir <- system.file("extdata", package="minfiData")
targets <- read.metharray.sheet(baseDir)
data <- summarize(targets)

bbmri-nl/MethylAid documentation built on May 31, 2019, 5:10 p.m.