Detection of Differentially Methylated Regions


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Documentation for package ‘DMRScan’ version 1.4.6

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as.GRanges Cast to GRranges
as.GRanges-method Cast to GRranges
dmrscan DMR Scan function
DMRScan.methylationData DMRScan
DMRScan.phenotypes DMRScan
estimateThreshold EstimateWindowThresholds
estimateWindowThreshold EstimateWindowThresholds
getRegions Method getRegions
getRegions-method Method getRegions
head-method Cat the head of a list of regions in a RegionList object
length-method Calculate the length of a region in terms of CpGs
makeCpGgenes Cluster
makeCpGregions Cluster
makeRegions Cluster
manyWindowSizeScanner Method Fixed window size scan for a sequence of window sizes
manyWindowSizeScanner-method Method Fixed window size scan for a sequence of window sizes
names-method Get the names of all probes within a region
nCpG Method nCpG
nCpG-method Method nCpG
oneWindowSizeScanner Method Fixed window size scan for one window size
oneWindowSizeScanner-method Method Fixed window size scan for one window size
pos Method pos
pos-method Method pos
print-method Print a region
pVal Method get pvalue
pVal-method Method get pvalue
range-method Get the genomic position of a Region
Region Shorthand for initializing region
Region-class Object of type Region
RegionList Shorthand for initializing RegionList
RegionList-class Class RegionList Class 'RegionList' is a collection of Regions
Rt Method Fixed window size scan for one window size
Rt-method Method Fixed window size scan for one window size
setRegion Method setRegion
setRegion-method Method setRegion
show-method Show a region
sort-method Sort a set of regions on p-value in a RegionList object
St Method Fixed window size scan for a sequence of window sizes
tVal Method get T statistic for a region
tVal-method Method get T statistic for a region
[ Get Object Region
[-method Get Object Region
[[ Get Object Region
[[-method Get Object Region