Description Usage Arguments Value Flavor v1 Flavor v2 References See Also

Algorithms to fit the CalMaTe model for a single SNP.
*Note: These are internal functions of the package.
They should not be used elsewhere.*

1 2 3 | ```
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 indentified 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`

().

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.