spatialAdjust: Correct spatial artifacts
In charm: Analysis of DNA methylation data from CHARM microarrays
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Remove spatial artifacts from microarray data stored in TilingFeatureSet objects
Usage
1
spatialAdjust(dat, copy=TRUE, blockSize, theta = 1)
Arguments
dat
TilingFeatureSet
copy
Only relevant when using disk-backed objects. If TRUE a copy will be made leaving the original object (dat) unchanged. The input object will not be preserved if copy=FALSE
blockSize
The array is divided into a series of blockSize x blockSize rectangular blocks and the average signal level calculated for each. If blockSize is unspecified a size is chosen that gives about 1250 probes per block.
theta
smoothing parameter
Details
The array is divided into a set of blockSize x blockSize squares. A kernel smoother is then used to even out spatial artifacts.
Value
a TilingFeatureSet
Author(s)
Martin Aryee <aryee@jhu.edu>
Examples
1
# See normalizeBetweenSamples
charm documentation built on May 6, 2019, 2:29 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) Examples
Description
Remove spatial artifacts from microarray data stored in TilingFeatureSet objects
Usage
1 | spatialAdjust(dat, copy=TRUE, blockSize, theta = 1)
|
Arguments
dat |
TilingFeatureSet |
copy |
Only relevant when using disk-backed objects. If TRUE a copy will be made leaving the original object (dat) unchanged. The input object will not be preserved if copy=FALSE |
blockSize |
The array is divided into a series of blockSize x blockSize rectangular blocks and the average signal level calculated for each. If blockSize is unspecified a size is chosen that gives about 1250 probes per block. |
theta |
smoothing parameter |
Details
The array is divided into a set of blockSize x blockSize squares. A kernel smoother is then used to even out spatial artifacts.
Value
a TilingFeatureSet
Author(s)
Martin Aryee <aryee@jhu.edu>
Examples
1 | # See normalizeBetweenSamples
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.