summarize {MethylAid} | R Documentation

## summarization of Illumina Human DNA Methylation array data

### 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)

[Package MethylAid version 1.14.0 Index]