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

Description Usage Arguments Details Value Examples

Description

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

Usage

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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

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

## End(Not run)

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