This function calculates the alpha values for a selected chromosome
and plots the distribution of alpha values. The shape of the
distribution is indicative of the presence or absence of partially
methylated domains (PMDs).
Selected chromosome for which alpha values are calculated. Must be
one of the sequence levels of m.
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
The number of cores that are used for the
calculation (default 1).
nCGbin
The number of CpGs in each sliding window used to calculate
alpha (default 101). The default is highly recommended.
Value
No return value. The function creates a figure
showing the alpha distribution for the selected chromosome that 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)
#calculate alpha distribution for one chromosome
plotAlphaDistributionOneChr(m=meth.gr, chr.sel="chr22", num.cores=1)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MethylSeekR)
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: mhsmm
Loading required package: mvtnorm
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MethylSeekR/plotAlphaDistributionOneChr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotAlphaDistributionOneChr
> ### Title: Calculate and plot alpha distribution.
> ### Aliases: plotAlphaDistributionOneChr
>
> ### ** Examples
>
>
> library(MethylSeekR)
>
> # get chromosome lengths
> library("BSgenome.Hsapiens.UCSC.hg18")
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
> sLengths=seqlengths(Hsapiens)
>
> # read methylation data
> methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",
+ package="MethylSeekR")
> meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths)
reading methylome data
Read 200000 records
>
> #calculate alpha distribution for one chromosome
> plotAlphaDistributionOneChr(m=meth.gr, chr.sel="chr22", num.cores=1)
determining alpha distribution for chromosome: chr22
>
>
>
>
>
>
>
> dev.off()
null device
1
>