| Title: | Visual and interactive quality control of large Illumina DNA Methylation array data sets |
|---|---|
| Description: | A visual and interactive web application using RStudio's shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored. |
| Authors: | Maarten van Iterson [aut, cre], Elmar Tobi[ctb], Roderick Slieker[ctb], Wouter den Hollander[ctb], Rene Luijk[ctb] and Bas Heijmans[ctb] |
| Maintainer: | L.J.Sinke <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.39.0 |
| Built: | 2024-06-30 05:36:04 UTC |
| Source: | https://github.com/bioc/MethylAid |
Generate background data from a summarizedData-object
as.background(object) ## S4 method for signature 'summarizedData' as.background(object)as.background(object) ## S4 method for signature 'summarizedData' as.background(object)
object |
summarizedData-object |
Generates a background dataset can be used in the filter plots
list with background data for the filter plots
mvaniterson
Concatenates two summarizedData objects into one object
## S4 method for signature 'summarizedData,ANY' combine(x, y, by = c("identical", "overlap"))## S4 method for signature 'summarizedData,ANY' combine(x, y, by = c("identical", "overlap"))
x |
summarizedData-object |
y |
summarizedData-object |
by |
argument indicating how the targets information should be combined |
one summarizedData object
data(exampleData) combine(exampleData, exampleData)data(exampleData) combine(exampleData, exampleData)
Pre-summarizedData object on 500 450k Human Methylation samples. Can be used as input for visualize
exampleDataexampleData
summarizedData-object
Pre-summarizedData object on 500 450k Human Methylation samples.
data(exampleData) ## Not run: visualize(exampleData)data(exampleData) ## Not run: visualize(exampleData)
show method for summarized Illumina Human DNA Methylation array data
## S4 method for signature 'summarizedData' show(object)## S4 method for signature 'summarizedData' show(object)
object |
summarizedData object |
print short summary summarizedData object
data(exampleData) exampleDatadata(exampleData) exampleData
summarize is the main function when called all samples in the targets file will be summarized
summarize(targets, batchSize = -1, BPPARAM = NULL, rp.zero = TRUE, verbose = TRUE, file = NULL, ...)summarize(targets, batchSize = -1, BPPARAM = NULL, rp.zero = TRUE, verbose = TRUE, file = NULL, ...)
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 |
... |
optional arguments to read.metharray.exp, i.e. force=TRUE |
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.
summarized data is saved optionally returned
mvaniterson
library(minfiData) baseDir <- system.file("extdata", package="minfiData") targets <- read.metharray.sheet(baseDir) data <- summarize(targets)library(minfiData) baseDir <- system.file("extdata", package="minfiData") targets <- read.metharray.sheet(baseDir) data <- summarize(targets)
container for summarized Illumina Human DNA Methylation array data
targets:Object of class "data.frame"
containing targets information.
controls:Object of class "data.frame"
containing quality control probe information.
Rcontrols:Object of class "matrix"
containing quality control probe intensities for the Red channel.
Gcontrols:Object of class "matrix"
containing quality control probe intensities for the Grn channel.
DPfreq:Object of class "vector"
containing frequencies of probes above background.
MU:Object of class "matrix"
containing Methylated and Unmethylated internsities.
plotdata:Object of class "list"
containing data to make plotting efficient.
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, ...)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)library(minfiData) baseDir <- system.file("extdata", package="minfiData") targets <- read.metharray.sheet(baseDir) data <- summarize(targets) ## Not run: visualize(data) ## End(Not run)