segmentUMRsLMRs: Identify UMRs and LMRs
In LukasBurger/MethylSeekR: Segmentation of Bis-seq data

Description Usage Arguments Value Author(s) Examples

View source: R/segmentUMRsLMRs.R

This function identifies hypomethylated regions and classifies them into UMRs and LMRs.

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segmentUMRsLMRs(m, meth.cutoff = 0.5, nCpG.cutoff = 3, PMDs = NA,
pdfFilename, num.cores = 1, myGenomeSeq, seqLengths, nCpG.smoothing = 3,
minCover = 5)

`m`	GRanges object containing the methylation data.
`meth.cutoff`	Cut-off on methylation for calling hypomethylated regions.
`nCpG.cutoff`	Cut-off on the minimal number of CpGs for calling hypomethylated regions.
`PMDs`	GRanges object of PMDs. Set to either the return value of the function segmentPMDs (see example) or to NA if there are no PMDs (default).
`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.
`myGenomeSeq`	Genome sequence as BSgenome object.
`seqLengths`	A named vector indicating the chromosome lengths of the genome used.
`nCpG.smoothing`	The number of consecutive CpGs that the methylation levels are averaged over.
`minCover`	Only CpGs with a coverage of at least minCover reads will be used.

Returns a GRanges object containing all UMRs and LMRs with the following metadata values: the number of CpGs with a coverage of at least minCover per region (nCG.segmentation), the number of CpGs in the DNA sequence (nCG), the total number of reads that map to CpGs in the region (T), the total number of read that map to CpGs without conversion of the C (M), the mean methylation of the segment (pmeth), the median methylation of the segment (median.meth) and the type (UMR/LMR) of region (type). The function creates a figure showing the classification of regions into UMRs and LMRs based on the number of CpGs they contain. 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)

FDR.cutoff <- 5 
m.sel <- 0.5 
n.sel <- 3

#segment UMRs and LMRs, assuming no PMDs
UMRLMRsegments.gr <- segmentUMRsLMRs(m=meth.gr, meth.cutoff=m.sel,
nCpG.cutoff=n.sel, myGenomeSeq=Hsapiens, seqLengths=sLengths)