CGcount: Determining the count of CpG dinucleotides for a set of...
In MEDME: Modelling Experimental Data from MeDIP Enrichment
Description
Usage
Arguments
Details
Value
See Also
Examples
Description
The count of CpGs is determined in each window of size wsize, with or withouth weighting, for each probe according to its position, chromosome and genome realease
Usage
1
Arguments
data
An object of class MEDMEset
wsize
number; the size of the smoothing window, in bp
wFunction
string; the type of weighting function, to choose among linear, exp, log or none
Details
Only human and mouse are currently supported. The respective genomic sequence metadata library needs to be downloaded from the Bioconductor website, installed and loaded (around 800Mb). Please
note that only the last genome release should be used. LiftOver UCSC tool could be used for batch conversion of old genomic position to the last genome release.
Value
An object of class MEDMEset is returned where the count of CpGs for each probe has been saved on the CGcount slot.
See Also
Examples
1
2
3
4
5
data(testMEDMEset)
## just an example with the first 1000 probes
testMEDMEset = smooth(data = testMEDMEset[1:1000,])
library(BSgenome.Hsapiens.UCSC.hg18)
testMEDMEset = CGcount(data = testMEDMEset)
MEDME documentation built on Nov. 8, 2020, 5:31 p.m.
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Description Usage Arguments Details Value See Also Examples
Description
The count of CpGs is determined in each window of size wsize, with or withouth weighting, for each probe according to its position, chromosome and genome realease
Usage
1 |
Arguments
data |
An object of class MEDMEset |
wsize |
number; the size of the smoothing window, in bp |
wFunction |
string; the type of weighting function, to choose among linear, exp, log or none |
Details
Only human and mouse are currently supported. The respective genomic sequence metadata library needs to be downloaded from the Bioconductor website, installed and loaded (around 800Mb). Please note that only the last genome release should be used. LiftOver UCSC tool could be used for batch conversion of old genomic position to the last genome release.
Value
An object of class MEDMEset is returned where the count of CpGs for each probe has been saved on the CGcount slot.
See Also
Examples
1 2 3 4 5 | data(testMEDMEset)
## just an example with the first 1000 probes
testMEDMEset = smooth(data = testMEDMEset[1:1000,])
library(BSgenome.Hsapiens.UCSC.hg18)
testMEDMEset = CGcount(data = testMEDMEset)
|
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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