calculateFDRs {MethylSeekR} | R Documentation

## Determine false discovery rate

### Description

This function calculates the false discovery rate (FDR) based on randomized Bis-seq data.

### Usage

    calculateFDRs(m, CGIs, PMDs = NA, pdfFilename=NULL, num.cores = 1,
    nCpG.smoothing = 3, meth.cutoffs = seq(0.3, 0.7, by=0.1), nCpG.cutoffs =
    seq(1, 6, by=1), minCover = 5)

### Arguments

`m` | GRanges object containing the methylation data.
`CGIs` | A GRanges object of CpG island coordinates. All CpGs overlapping CpG islands will be removed for the randomization.
`PMDs` | The GRanges object of the PMDs. Set to either the return value of the function segmentPMDs (see example) or to NA (default) if there are no PMDs.
`pdfFilename` | Name of the pdf file in which the figure is saved. If no name is provided (default), the figure is printed to the screen.
`num.cores` | Number of cores used for the calculations.
`nCpG.smoothing` | The number of consecutive CpGs that the methylation levels are averaged over.
`meth.cutoffs` | A vector containing the cut-offs in methylation for which the FDR should be calculated. Numbers must be between 0 and 1.
`nCpG.cutoffs` | A vector containing the cut-offs on the minimal number of CpGs per region for which the FDR should be calculated.
`minCover` | Only CpGs with a coverage of at least minCover reads will be used.

### Value

A list containing a matrix with FDR values and a matrix with the number of inferred segments for each methylation cut-off (rows) and each cut-off on the minimal number of CpGs per region (columns). The function creates a figure showing the relationship between the methylation cut-off, the cut-off on the minimal number of CpGs per region, the number of inferred segments and the FDR. The figure is either printed to the screen (default) or saved as a pdf if a filename is provided.

### Author(s)

Lukas Burger lukas.burger@fmi.ch

### Examples

    library(MethylSeekR)

    # get chromosome lengths
    library("BSgenome.Hsapiens.UCSC.hg18")
    sLengths=seqlengths(Hsapiens)

    # read methylation data
    methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",
    package="MethylSeekR")
    meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths)

    #load CpG islands
    library(rtracklayer)
    session <- browserSession()
    genome(session) <- "hg18"
    query <- ucscTableQuery(session, "cpgIslandExt")
    CpGislands.gr <- track(query)
    genome(CpGislands.gr) <- NA
    CpGislands.gr <- resize(CpGislands.gr, 5000, fix="center")

    #calculate FDRs, assuming no PMDs
    stats <- calculateFDRs(m=meth.gr, CGIs=CpGislands.gr)

[Package MethylSeekR version 1.20.0 Index]