summarization of Illumina Human DNA Methylation array data

Share:

Description

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

Usage

1
2
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

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

1
2
3
4
library(minfiData)
baseDir <- system.file("extdata", package="minfiData")
targets <- read.metharray.sheet(baseDir)
data <- summarize(targets)