printEstProfile {mBPCR} | R Documentation |
Function to print the results of the profile estimation of copy number data
printEstProfile(path='', sampleName='', snpName, chr, position, logratio, chrToBePrinted, estPC, estBoundaries=NULL, postProbT=NULL, regrCurve=NULL, regr=NULL)
path |
path of the folder where the user wants to print the results of the estimation (it must end with '\\' in windows, or '//' in linux). If path='', they will be printed in the working directory |
sampleName |
name of the sample. If the name of the sample if provided, it is used to named the printed files. |
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 |
chrToBePrinted |
array containing the name of the estimated chromosomes, that the user wants to print. 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 |
estBoundaries |
list containing the vectors of the estimated breakpoints, for each of the chromosomes mentioned in chrToBePrinted . If estBoundaries=NULL , then this information is not printed. |
postProbT |
list containing the vectors of the posterior probabilities to be a breakpoint of the estimated breakpoints, for each of the chromosomes mentioned in chrToBePrinted . If postProbT=NULL ,
then this information is not printed in the file containing the estimated breakpoints. |
regrCurve |
array containing the estimated regression curve. If regrCurve=NULL , then the file containing this information is not printed. |
regr |
choice of the computation of the regression curve. If regr=NULL , then the regression curve was not computed (then the file containing this information is not printed),
if regr=1 the Bayesian Regression Curve with K_2 was computed (BRC with K_2),
if regr=2 the Bayesian Regression Curve Averaging over k was computed (BRCAk). |
The function print at maximum three files:
estBoundaries=NULL
.regrCurve=NULL
.##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 the global parameters param <- estGlobParam(rec10k$logratio) ##estimation of chromosome 3 results=computeMBPCR(rec10k$logratio[which(rec10k$chr == 3)], nu=param$nu, rhoSquare=param$rhoSquare, sigmaSquare=param$sigmaSquare) ##print the estimated profile of chromosome 3 estPC <- array(dim=length(rec10k$snpName)) estBoundaries <- list(dim=1) postProbT <- list(dim=1) estPC[rec10k$chr == 3] <- results$estPC estBoundaries[[1]] <- results$estBoundaries postProbT[[1]] <- c(results$postProbT[results$estBoundaries[-results$estK]],1) printEstProfile(path='', sampleName='rec10k', rec10k$snpName, rec10k$chr, rec10k$position, rec10k$logratio, chrToBePrinted=3, estPC, estBoundaries, postProbT)[Package mBPCR version 1.0 Index]