plotEstProfile {mBPCR} | R Documentation |
Function to plot the estimated profiles of copy number data. The function gives also the possibility to print each graph on a file.
plotEstProfile(path='', sampleName='', chr, position, logratio, chrToBePlotted, estPC, maxProbeNumber, legendPosition='bottomleft', regrCurve=NULL, regr=NULL)
path |
path of the folder where the user wants to print the plots of the estimated profiles (it must end with '\\' in windows, or '//' in linux). If path='', they will be printed in the working directory,
while if path=NULL , the plots will not be printed. |
sampleName |
name of the sample, if the user wants to put it in the name of the files printed |
snpName |
array containing the name of each probe |
chr |
array containing the name of the chromosome to which each probe belongs |
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: an integer from 1 to 22 and 'X'. |
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 plotte),
if regr=1 the Bayesian Regression Curve was computed (mBRC with K_2),
if regr=2 the Bayesian Regression Curve Averaging over k was computed (BRCAk). |
The function plots the estimated profiles of the chromosomes of chrToBePlotted
, separately. Eventually, the function prints the same plots in .eps format.
##import the 10K data of cell line REC ##for windows path <- 'data\\rec10k.dat' ##for linux ##path <- 'data//rec10k.dat' rec10k <- importCNData(path, NRowSkip=1) ##estimation of chromosomes 2, 3 and 4 results <- estProfileWithMBPCR(path='', sampleName='rec10k', rec10k$snpName, rec10k$chr, rec10k$position, rec10k$logratio, chrToBeAnalyzed=2:4, maxProbeNumber=2000) ##plot the corresponding estimated profiles (the graphs are also printed in the working directory) plotEstProfile(path='', sampleName='rec10k', rec10k$chr, rec10k$position, rec10k$logratio, chrToBePlotted=2:4, results$estPC, maxProbeNumber=2000)[Package mBPCR version 1.0 Index]