Detection of Differentially Methylated Regions


[Up] [Top]

Documentation for package ‘DMRScan’ version 1.0.0

Help Pages

DMRScan_package-package DMRScan: An R-package for identification of Differentially Metylated Regions
DMRScan DMR Scan function
DMRscan DMR Scan function
DMRScan.methylationData DMRScan
DMRScan.phenotypes DMRScan
DMRScan_package DMRScan: An R-package for identification of Differentially Metylated Regions
estimateThreshold Estimate window thresholds
estimateWindowThreshold Estimate window thresholds
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
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
plot Plot DMRs of type Region
plot.Region Plot DMRs of type Region
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