fitCalMaTeInternal | R Documentation |
Algorithms to fit the CalMaTe model for a single SNP. Note: These are internal functions of the package. They should not be used elsewhere.
fitCalMaTeV1(dataT, references, fB1=1/3, fB2=2/3, maxIter=50, ...) fitCalMaTeV2(dataT, references, fB1=1/3, fB2=2/3, maxIter=50, ...) fitCalMaTeMedians(dataT, references, fB1=1/3, fB2=2/3,...)
dataT |
A 2xI |
references |
A |
fB1, fB2 |
Thresholds for calling genotypes AA, AB, BB from the allele B fractions. |
maxIter |
The maximum number of iterations without converging before the algorithm quits. |
... |
Not used. |
Returns a 2xI numeric
matrix
of calibrated ASCNs.
This is an early version (June 2010-January 2012) of the algorithm described in [1].
This is the model and algorithm described in [1].
This version was introduced to decrease the number of "artificial outliers" introduced by CalMaTe for some SNPs due to non-converging or wreak-havoc estimates of the SNP effects. Flavor v2 differ from Flavor v1 as follows:
The estimation of the model parameters are now done solely based on reference samples. In previous versions, some of the initial estimation steps were using also non-reference samples.
For a small number of SNPs, the main CalMaTe scheme for estimating
parameters would not converge or converge poorly. For such SNPs
CalMaTe now falls back to using a plain median estimator,
i.e. fitCalMaTeMedians()
.
The above fallback estimator is also used in cases where all samples are identified to be homozygous.
The fitCalMaTeMedians()
method is used as a fallback method
by fitCalMaTeV2()
. It fits CalMaTe without using the
rlm
function.
[1] M. Ortiz-Estevez, A. Aramburu, H. Bengtsson, P. Neuvial and A. Rubio, CalMaTe: A method and software to improve allele-specific copy number of SNP arrays for downstream segmentation, Bioinformatics, 2012 [PMC3381965].
These functions are called by calmateByThetaAB
().
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.