an INPUT SET (i.e. a MEDIPS SET created from Input sequening data)
CSet
an according COUPLING SET object
plot_chr
default="all". It is recommended to call a graphics device (e.g. png("calibrationPlot.png")) before calling the plot command, because R might not be able to plot the full amount of data in reasonable time.
rpkm
can be either TRUE or FALSE. If set to TRUE, the methylation signals will be transformed into rpkm before plotted.
The coupling values remain untouched. It is necessary to set rpkm=T, if both, a MSet and an ISet are given and plotted at the same time.
main
The title of the calibration plot.
xrange
The signal range of the calibration curve typically falls into a low signal range.
By setting the xrange parameter to TRUE, the calibration plot will visualize the low signal range only.
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(MEDIPS)
Loading required package: BSgenome
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: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
Loading required package: Rsamtools
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MEDIPS/MEDIPS.plotCalibrationPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MEDIPS.plotCalibrationPlot
> ### Title: Creates the calibration plot.
> ### Aliases: MEDIPS.plotCalibrationPlot
>
> ### ** Examples
>
> library(MEDIPSData)
> data(hESCs_MeDIP)
> data(CS)
>
> MEDIPS.plotCalibrationPlot(CSet=CS, main="Calibration Plot", MSet=hESCs_MeDIP[[1]], plot_chr="chr22", rpkm=TRUE, xrange=TRUE)
Calculating calibration curve...
Performing linear regression...
Intercept: 0.498483378520726
Slope: 0.410973722142348
Extracting data for chr22 ...
Calculating genomic coordinates...
Creating Granges object for genome wide windows...
Plotting calibration plot for chr22 ...
>
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.