getControlIndex: Get indices of control probes from CpG-free regions
In charm: Analysis of DNA methylation data from CHARM microarrays
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
Get indices of control probes from CpG-free regions.
Usage
1
getControlIndex(dat, controlProbes = NULL, noCpGWindow = 1000, subject, onlyGood = FALSE, matrix = TRUE)
Arguments
dat
TilingFeatureSet
controlProbes
vector of names used to denote control probes in the 'container' column of the Nimblegen annotation (ndf) file. Optional
noCpGWindow
Size of the window centered on the probe that must be CpG-free
subject
A BSgenome object
onlyGood
deprecated option
matrix
deprecated option
Details
The probes can either be identified as control probes in the microarray annotation package, or alternatively the function will search the genome (given an appropriate BSgenome object) for suitable probes.
Value
a vector
Author(s)
Martin Aryee <aryee@jhu.edu>
Examples
1
# See dmrFdr
charm documentation built on May 6, 2019, 2:29 a.m.
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Description Usage Arguments Details Value Author(s) Examples
Description
Get indices of control probes from CpG-free regions.
Usage
1 | getControlIndex(dat, controlProbes = NULL, noCpGWindow = 1000, subject, onlyGood = FALSE, matrix = TRUE)
|
Arguments
dat |
TilingFeatureSet |
controlProbes |
vector of names used to denote control probes in the 'container' column of the Nimblegen annotation (ndf) file. Optional |
noCpGWindow |
Size of the window centered on the probe that must be CpG-free |
subject |
A BSgenome object |
onlyGood |
deprecated option |
matrix |
deprecated option |
Details
The probes can either be identified as control probes in the microarray annotation package, or alternatively the function will search the genome (given an appropriate BSgenome object) for suitable probes.
Value
a vector
Author(s)
Martin Aryee <aryee@jhu.edu>
Examples
1 | # See dmrFdr
|
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.
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