filterDMRs {DMRcaller} | R Documentation |
This function verifies whether a set of pottential DMRs (e.g. genes, transposons, CpG islands) are differentially methylated or not.
filterDMRs(methylationData1, methylationData2, potentialDMRs, context = "CG", test = "fisher", pValueThreshold = 0.01, minCytosinesCount = 4, minProportionDifference = 0.4, minReadsPerCytosine = 3, cores = 1)
methylationData1 |
the methylation data in condition 1
(see |
methylationData2 |
the methylation data in condition 2
(see |
potentialDMRs |
a |
context |
the context in which the DMRs are computed ( |
test |
the statistical test used to call DMRs ( |
pValueThreshold |
DMRs with p-values (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
|
minReadsPerCytosine |
DMRs with the average number of reads lower than
|
cores |
the number of cores used to compute the DMRs. |
a GRanges
object with 11 metadata columns that contain
the DMRs; see computeDMRs
.
Nicolae Radu Zabet
DMRsNoiseFilterCG
, computeDMRs
,
analyseReadsInsideRegionsForCondition
and mergeDMRsIteratively
# load the methylation data data(methylationDataList) # load the gene annotation data data(GEs) #select the genes genes <- GEs[which(GEs$type == "gene")] # the regions where to compute the DMRs regions <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E5)) genes <- genes[overlapsAny(genes, regions)] # filter genes that are differntially methylated in the two conditions DMRsGenesCG <- filterDMRs(methylationDataList[["WT"]], methylationDataList[["met1-3"]], potentialDMRs = genes, context = "CG", test = "score", pValueThreshold = 0.01, minCytosinesCount = 4, minProportionDifference = 0.4, minReadsPerCytosine = 3, cores = 1)