visualize: visualize the summarized Illumina Human DNA Methylation array...

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

Description

launch a shiny app for visualization of the summarized Illumina Human DNA Methylation array data

Usage

visualize(object, thresholds = list(hm450k = list(MU = 10.5, OP = 11.75, BS =
  12.75, HC = 13.25, DP = 0.95), epic = list(MU = 10, OP = 12, BS = 11.75, HC =
  12.75, DP = 0.95)), background = NULL, ...)

## S4 method for signature 'summarizedData'
visualize(object, thresholds = list(hm450k =
  list(MU = 10.5, OP = 11.75, BS = 12.75, HC = 13.25, DP = 0.95), epic = list(MU
  = 10, OP = 12, BS = 11.75, HC = 12.75, DP = 0.95)), background = NULL, ...)

Arguments

object	summarizedData object
thresholds	default thresholds
background	optional summarizedData-object used as background in filter control plots
...	for future use

Details

Outliers are detected based on a set of default thresholds. To use a use-defined set of thresholds use the thresholds argument.

Value

lauches a web browser with the shiny application and returns a data.frame with detected outliers

Examples

library(minfiData)
baseDir <- system.file("extdata", package="minfiData")
targets <- read.metharray.sheet(baseDir)
data <- summarize(targets)
## Not run: 
visualize(data)

## End(Not run)

MethylAid documentation built on Nov. 8, 2020, 8:20 p.m.