computeMBPCR
(Package: mBPCR) :
Estimate the copy number profile
Function to estimate the copy number profile with a piecewise constant function using mBPCR. Eventually, it is possible to estimate the profile with a smoothing curve using either the Bayesian Regression Curve with K_2 (BRC with K_2) or the Bayesian Regression Curve Averaging over k (BRCAk). It is also possible to choose the estimator of the variance of the levels rhoSquare (i.e. either hat{ρ}_1^2 or hat{ρ}^2) and by default hat{ρ}_1^2 is used.
● Data Source:
BioConductor
● Keywords: regression, smooth
● Alias: computeMBPCR
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1 images
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estGlobParam
(Package: mBPCR) :
Estimate global parameters of copy number data
Function to estimate the global parameters of copy number data: the mean and the variance of the segment levels (called nu and rhoSquare, respectively), the variance of the noise (sigmaSquare). It is possible to choose the estimator of rhoSquare (i.e. either hat{ρ}_1^2 or hat{ρ}^2) and by default hat{ρ}_1^2 is used.
● Data Source:
BioConductor
● Keywords: univar
● Alias: estGlobParam
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0 images
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estProfileWithMBPCR
(Package: mBPCR) :
Estimate and print the copy number profile of some chromosomes of a sample
Function to estimate the copy number profile with a piecewise constant function using mBPCR. Eventually, it is possible to estimate the profile with a smoothing curve, using either the Bayesian Regression Curve with K_2 (BRC with K_2) or the Bayesian Regression Curve Averaging over k (BRCAk). It is also possible to choose the estimator of the variance of the levels rhoSquare (i.e. either hat{ρ}_1^2 or hat{ρ}^2) and by default hat{ρ}_1^2 is used.
● Data Source:
BioConductor
● Keywords: regression, smooth
● Alias: estProfileWithMBPCR
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1 images
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estProfileWithMBPCRforOligoSnpSet
(Package: mBPCR) :
Estimate and print the copy number profile of some chromosomes of samples in an oligoSnpSet object
Function to estimate the copy number profile with a piecewise constant function using mBPCR. Eventually, it is possible to estimate the profile with a smoothing curve, using either the Bayesian Regression Curve with K_2 (BRC with K_2) or the Bayesian Regression Curve Averaging over k (BRCAk). It is also possible to choose the estimator of the variance of the levels rhoSquare (i.e. either hat{ρ}_1^2 or hat{ρ}^2) and by default hat{ρ}_1^2 is used.
● Data Source:
BioConductor
● Keywords: regression, smooth
● Alias: estProfileWithMBPCRforOligoSnpSet
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0 images
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importCNData
(Package: mBPCR) :
Import the copy number data
Function to import the raw copy number data from a tab delimited file.
● Data Source:
BioConductor
● Keywords: file
● Alias: importCNData
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1 images
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logAdd
(Package: mBPCR) :
Overflow-safe computation of the logarithm of a sum
Function to compute the logarithm of a sum of small numbers, avoiding overflow.
● Data Source:
BioConductor
● Keywords: math
● Alias: logAdd
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mBPCR-internal
(Package: mBPCR) :
Internal mBPCR functions
Internal functions of package mBPCR.
● Data Source:
BioConductor
● Keywords: internal
● Alias: computeA10, computeLA0Vect, computePCReg, computeRecursions, computeRegrCurve, indexLA0
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plotEstProfile
(Package: mBPCR) :
Plot the estimated profile of copy number data
Function to plot the estimated profiles of copy number data.
● Data Source:
BioConductor
● Keywords: hplot, print
● Alias: plotEstProfile
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1 images
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writeEstProfile
(Package: mBPCR) :
Write the estimated profile of copy number data
Function to write nicely the results of the copy number profile estimation. The function either writes the tables directly on a tab delimited file or returns the corresponding tables.
● Data Source:
BioConductor
● Keywords: file
● Alias: writeEstProfile
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