visualize {MethylAid} | R Documentation

## visualize the summarized Illumina Human DNA Methylation array data

### 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)

[Package MethylAid version 1.18.0 Index]