visualize {MethylAid} | R Documentation |
launch a shiny app for visualization of the summarized Illumina Human DNA Methylation array data
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, ...)
object |
summarizedData object |
thresholds |
default thresholds |
background |
optional summarizedData-object used as background in filter control plots |
... |
for future use |
Outliers are detected based on a set of default thresholds. To use a use-defined set of thresholds use the thresholds argument.
lauches a web browser with the shiny application and returns a data.frame with detected outliers
library(minfiData) baseDir <- system.file("extdata", package="minfiData") targets <- read.metharray.sheet(baseDir) data <- summarize(targets) ## Not run: visualize(data) ## End(Not run)