Compute DMRs
Description
This function computes the differentially methylated regions between two conditions.
Usage
1 2 3 4 5 6  computeDMRs(methylationData1, methylationData2, regions = NULL,
context = "CG", method = "noise_filter", windowSize = 100,
kernelFunction = "triangular", lambda = 0.5, binSize = 100,
test = "fisher", pValueThreshold = 0.01, minCytosinesCount = 4,
minProportionDifference = 0.4, minGap = 200, minSize = 50,
minReadsPerCytosine = 4, cores = 1)

Arguments
methylationData1 
the methylation data in condition 1
(see 
methylationData2 
the methylation data in condition 2
(see 
regions 
a 
context 
the context in which the DMRs are computed ( 
method 
the method used to compute the DMRs ( 
windowSize 
the size of the triangle base measured in nucleotides.
This parameter is required only if the selected method is

kernelFunction 
a 
lambda 
numeric value required for the Gaussian filter
( 
binSize 
the size of the tiling bins in nucleotides. This parameter is
required only if the selected method is 
test 
the statistical test used to call DMRs ( 
pValueThreshold 
DMRs with pvalues (when performing the statistical
test; see 
minCytosinesCount 
DMRs with less cytosines in the specified context
than 
minProportionDifference 
DMRs where the difference in methylation
proportion between the two conditions is lower than

minGap 
DMRs separated by a gap of at least 
minSize 
DMRs with a size smaller than 
minReadsPerCytosine 
DMRs with the average number of reads lower than

cores 
the number of cores used to compute the DMRs. 
Value
the DMRs stored as a GRanges
object with the following
metadata columns:
 direction
a number indicating whether the region lost (1) or gain (+1) methylation in condition 2 compared to condition 1.
 context
the context in which the DMRs was computed (
"CG"
,"CHG"
or"CHH"
). sumReadsM1
the number of methylated reads in condition 1.
 sumReadsN1
the total number of reads in condition 1.
 proportion1
the proportion methylated reads in condition 1.
 sumReadsM2
the number of methylated reads in condition 2.
 sumReadsN2
the total number reads in condition 2.
 proportion2
the proportion methylated reads in condition 2.
 cytosinesCount
the number of cytosines in the DMR.
 regionType
a string indicating whether the region lost (
"loss"
) or gained ("gain"
) methylation in condition 2 compared to condition 1. pValue
the pvalue (adjusted to control the false discovery rate with the Benjamini and Hochberg's method) of the statistical test when the DMR was called.
Author(s)
Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang
See Also
filterDMRs
, mergeDMRsIteratively
,
analyseReadsInsideRegionsForCondition
and
DMRsNoiseFilterCG
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36  # load the methylation data
data(methylationDataList)
# the regions where to compute the DMRs
regions < GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E5))
# compute the DMRs in CG context with noise_filter method
DMRsNoiseFilterCG < computeDMRs(methylationDataList[["WT"]],
methylationDataList[["met13"]], regions = regions,
context = "CG", method = "noise_filter",
windowSize = 100, kernelFunction = "triangular",
test = "score", pValueThreshold = 0.01,
minCytosinesCount = 4, minProportionDifference = 0.4,
minGap = 200, minSize = 50, minReadsPerCytosine = 4,
cores = 1)
## Not run:
# compute the DMRs in CG context with neighbourhood method
DMRsNeighbourhoodCG < computeDMRs(methylationDataList[["WT"]],
methylationDataList[["met13"]], regions = regions,
context = "CG", method = "neighbourhood",
test = "score", pValueThreshold = 0.01,
minCytosinesCount = 4, minProportionDifference = 0.4,
minGap = 200, minSize = 50, minReadsPerCytosine = 4,
cores = 1)
# compute the DMRs in CG context with bins method
DMRsBinsCG < computeDMRs(methylationDataList[["WT"]],
methylationDataList[["met13"]], regions = regions,
context = "CG", method = "bins", binSize = 100,
test = "score", pValueThreshold = 0.01, minCytosinesCount = 4,
minProportionDifference = 0.4, minGap = 200, minSize = 50,
minReadsPerCytosine = 4, cores = 1)
## End(Not run)
