mCsmoothing {methylPipe} | R Documentation |
Smoothing and plotting methylation data, even chromosome wide.
## S4 method for signature 'methylPipe,BSdata' mCsmoothing(Object, refgr, Scorefun='sum', Nbins=20, Context="CG", plot=TRUE)
Object |
An object of class BSdata |
refgr |
GRanges; Genomic Ranges to plot the data |
Scorefun |
character; either sum or mean for smoothing |
Nbins |
numeric; the number of interval each range is divided |
Context |
character; either all or a combination of CG, CHG, and CHH |
plot |
logical; whether the smoothed profile has to be plotted |
The sum or the mean methylation level is determined on each window of size Binsize and smoothed with the smooth.spline function.
A list with three components: pos (the left most point of each window), score (either the sum or the mean methylation levels), smoothed (the smoothed methylation levels).
Mattia Pelizzola
require(BSgenome.Hsapiens.UCSC.hg18) uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184))) H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe') H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens) gr <- GRanges("chr20",IRanges(1,5e5)) sres <- mCsmoothing(H1.db, gr, Scorefun='sum', Nbins=50, Context="CG", plot=TRUE)