getRepeatScores-RepeatEpigenomeCollection-method: getRepeatScores-methods
In MPIIComputationalEpigenetics/epiRepeatR: epiRepeatR
Description
Usage
Arguments
Value
Author(s)
Description
Retrieve values of epigenetic quantifications for each RE in each sample
Usage
1
2
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4
## S4 method for signature 'RepeatEpigenomeCollection'
getRepeatScores(.Object, mark,
dropEmptySamples = FALSE,
minCpGcov = getConfigElement("meth.minCpGcov"))
Arguments
.Object
RepeatEpigenomeCollection object
mark
Epigenetic mark for which the score information is retrieved
dropEmptySamples
Logical indicating whether samples in which the mark is not present should be dropped
minCpGcov
[DNAmeth only] number of reads covering each CpG in order for it to be considered in the
mean methylation level
Value
A matrix of dimension numRE X numSamples containing scores. Scores are mean methylation levels for DNA methylation and
log2 of the fold change for enrichment based methods.
Author(s)
Fabian Mueller
MPIIComputationalEpigenetics/epiRepeatR documentation built on March 22, 2021, 11:09 p.m.
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Description Usage Arguments Value Author(s)
Description
Retrieve values of epigenetic quantifications for each RE in each sample
Usage
1 2 3 4 | ## S4 method for signature 'RepeatEpigenomeCollection'
getRepeatScores(.Object, mark,
dropEmptySamples = FALSE,
minCpGcov = getConfigElement("meth.minCpGcov"))
|
Arguments
.Object |
|
mark |
Epigenetic mark for which the score information is retrieved |
dropEmptySamples |
Logical indicating whether samples in which the mark is not present should be dropped |
minCpGcov |
[ |
Value
A matrix of dimension numRE X numSamples containing scores. Scores are mean methylation levels for DNA methylation and log2 of the fold change for enrichment based methods.
Author(s)
Fabian Mueller
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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