plotEstProfile: Plot the estimated profile of copy number data

In paolarancoita/mBPCR: Bayesian Piecewise Constant Regression for DNA copy number estimation

Description

Function to plot the estimated profiles of copy number data.

Usage

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

Arguments

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'.

Details

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

Examples

##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)

paolarancoita/mBPCR documentation built on Jan. 12, 2020, 6:24 p.m.