computeMethylationProfile {DMRcaller} | R Documentation |
This function computes the low resolution profiles for the bisulfite sequencing data.
computeMethylationProfile(methylationData, region, windowSize = floor(width(region)/500), context = "CG")
methylationData |
the methylation data stored as a |
region |
a |
windowSize |
a |
context |
the context in which the DMRs are computed ( |
a GRanges
object with equal sized tiles of the
region
. The object consists of the following metadata
the number of methylated reads.
the total number of reads.
the proportion of methylated reads.
the context ("CG"
, "CHG"
or "CHH"
).
Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang
plotMethylationProfileFromData
,
plotMethylationProfile
, methylationDataList
# load the methylation data data(methylationDataList) # the region where to compute the profile region <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E6)) # compute low resolution profile in 20 Kb windows lowResProfileWTCHH <- computeMethylationProfile(methylationDataList[["WT"]], region, windowSize = 20000, context = "CHH") ## Not run: # compute low resolution profile in 10 Kb windows lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]], region, windowSize = 10000, context = "CG") lowResProfileMet13CG <- computeMethylationProfile( methylationDataList[["met1-3"]], region, windowSize = 10000, context = "CG") ## End(Not run)