Filter DMRs

Description

This function verifies whether a set of pottential DMRs (e.g. genes, transposons, CpG islands) are differentially methylated or not.

Usage

1
2
3
filterDMRs(methylationData1, methylationData2, potentialDMRs, context = "CG",
  test = "fisher", pValueThreshold = 0.01, minCytosinesCount = 4,
  minProportionDifference = 0.4, minReadsPerCytosine = 3, cores = 1)

Arguments

methylationData1

the methylation data in condition 1 (see methylationDataList).

methylationData2

the methylation data in condition 2 (see methylationDataList).

potentialDMRs

a GRanges object with potential DMRs where to compute the DMRs. This can be a a list of gene and/or transposable elements coordinates.

context

the context in which the DMRs are computed ("CG", "CHG" or "CHH").

test

the statistical test used to call DMRs ("fisher" for Fisher's exact test or "score" for Score test).

pValueThreshold

DMRs with p-values (when performing the statistical test; see test) higher or equal than pValueThreshold are discarded. Note that we adjust the p-values using the Benjamini and Hochberg's method to control the false discovery rate.

minCytosinesCount

DMRs with less cytosines in the specified context than minCytosinesCount will be discarded.

minProportionDifference

DMRs where the difference in methylation proportion between the two conditions is lower than minProportionDifference are discarded.

minReadsPerCytosine

DMRs with the average number of reads lower than minReadsPerCytosine are discarded.

cores

the number of cores used to compute the DMRs.

Value

a GRanges object with 11 metadata columns that contain the DMRs; see computeDMRs.

Author(s)

Nicolae Radu Zabet

See Also

DMRsNoiseFilterCG, computeDMRs, analyseReadsInsideRegionsForCondition and mergeDMRsIteratively

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
# 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)