calculateFDRs {MethylSeekR} | R Documentation |
This function calculates the false discovery rate (FDR) based on randomized Bis-seq data.
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)
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. |
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.
Lukas Burger lukas.burger@fmi.ch
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, table = "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)