An RGChannelSet, a MethylSet or a
matrix. We either use the getBeta (or getM for
measure="M") function to get Beta values (or M-values) (for
the first two) or we assume the matrix contains Beta values (or
M-values).
cpg
A character vector of the CpG position identifiers to be plotted.
pheno
A vector of phenotype values.
type
Is the phenotype categorical or continuous?
measure
Should Beta values or log-ratios (M) be plotted?
ylim
y-axis limits.
ylab
y-axis label.
xlab
x-axis label.
fitLine
Fit a least-squares best fit line when using a continuous phenotype.
mainPrefix
Text to prepend to the CpG name in the plot main title.
mainSuffix
Text to append to the CpG name in the plot main title.
Details
This function plots methylation values (Betas or log-ratios) at
individual CpG loci as a function of a phenotype.
Value
No return value. Plots are produced as a side-effect.
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.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
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(minfi)
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: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: lattice
Loading required package: GenomicRanges
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: SummarizedExperiment
Loading required package: Biostrings
Loading required package: XVector
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/minfi/plotCpg.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotCpg
> ### Title: Plot methylation values at an single genomic position
> ### Aliases: plotCpg
>
> ### ** Examples
>
> if (require(minfiData)) {
+
+ grp <- pData(MsetEx)$Sample_Group
+ cpgs <- c("cg00050873", "cg00212031", "cg26684946", "cg00128718")
+ par(mfrow=c(2,2))
+ plotCpg(MsetEx, cpg=cpgs, pheno=grp, type="categorical")
+
+ }
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
>
>
>
>
>
> dev.off()
null device
1
>