plotEstProfile: Plot the estimated profile of copy number data
In mBPCR: Bayesian Piecewise Constant Regression for DNA copy number estimation

Description Usage Arguments Details Examples

Function to plot the estimated profiles of copy number data.

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  plotEstProfile(sampleName='', chr, position, logratio, chrToBePlotted, estPC, 
                 maxProbeNumber, legendPosition='bottomleft', regrCurve=NULL, 
                 regr=NULL, hg='hg18')

`sampleName`	name of the sample, if the user wants to put it in the title of the graph
`chr`	array containing the name of the chromosome to which each probe belongs. The possible values of the elements of `chr` are: the integers from 1 to 22, 'X' and 'Y'.
`position`	array containing the physical position of each probe
`logratio`	array containing the log2ratio of the raw copy number data
`chrToBePlotted`	array containing the name of the estimated chromosomes, that the user wants to plot. The possible values of the chromosomes are: the integers from 1 to 22, 'X' and 'Y'.
`estPC`	array containing the estimated copy number profile as a piecewise constant function. If `estPC=NULL`, only the estimated Bayesian regression curve is plotted.
`maxProbeNumber`	maximum number of probes that a chromosome (or arm of a chromosome) can have to be analyzed. The procedure of profile estimation needs the computation of an array of length (length(chromosome)+1)(length(chromosome)+2)/2. To be sure to have set this parameter correctly, try to create the array `A <- array(1, dim=(maxProbeNumber+1)(maxProbeNumber+2)/2)`, before starting with the estimation procedure.
`legendPosition`	string containing the position of the legend in the plot. The possible values are the same used in the function `plot`.
`regrCurve`	array containing the estimated regression curve. If `regrCurve=NULL`, then the estimated Bayesian regression curve is not plotted. If `regrCurve!=NULL` and also `estPC!=NULL` both estimated profiles are plotted on the same graph.
`regr`	choice of the computation of the regression curve. If `regr=NULL`, then the regression curve was not computed (then the estimated Bayesian regression curve is not plotted), if `regr="BRC"` the Bayesian Regression Curve was computed (mBRC with K_2), if `regr="BRCAk"` the Bayesian Regression Curve Averaging over k was computed (BRCAk).
`hg`	genome build used for retrieving the base positions of the centromeres in case the chromosomes need to be divided into two parts for the estimation (see explanation of `maxProbeNumber`). Current available options are: `'hg18'`, `'hg19'` and `'hg38'`.

The function plots the estimated profiles of the chromosomes of chrToBePlotted, separately.

##import the 10K data of cell line REC
data(rec10k)
##estimation of chromosomes 3 and 5
results <- estProfileWithMBPCR(rec10k$SNPname, rec10k$Chromosome, rec10k$PhysicalPosition, 
rec10k$log2ratio, chrToBeAnalyzed=c(3,5), maxProbeNumber=2000)
##plot the corresponding estimated profiles
plotEstProfile(sampleName='rec10k', rec10k$Chromosome, rec10k$PhysicalPosition, rec10k$log2ratio, 
chrToBePlotted=c(3,5), results$estPC, maxProbeNumber=2000)