filterDMRs {DMRcaller} | R Documentation

## Filter DMRs

### Description

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

### Usage

    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

    # 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)

[Package DMRcaller version 1.19.0 Index]