Description Usage Arguments Value Author(s) See Also Examples

View source: R/crossvalFunctions.R

For a given data set, chromosome, class, and kernel function, this function helps in determining optimal settings for the kernel parameter(s). The performance of individual parameter setting is assessed by cross- validation.

1 2 3 |

`data` |
Gene expression data in the MACAT list format. See data(stjude) for an example. |

`class` |
Sample class to be analyzed |

`chromosome` |
Chromosome to be analyzed |

`kernel` |
Choose kernel to smooth scores along the chromosome. Available are 'kNN' for k-Nearest-Neighbors, 'rbf' for radial-basis-function (Gaussian), 'basePairDistance' for a kernel, which averages over all genes within a given range of base pairs around a position. |

`kernelparams` |
Additional parameters for the kernel as list, e.g., kernelparams=list(k=5) for taking the 5 nearest neighbours in the kNN-kernel. If NULL some defaults are set within the function. |

`paramMultipliers` |
Numeric vector. If you do cross-validation of the kernel parameters, specify these as multipliers of the given (standard) kernel parameter, depending on your kernel choice (see page 5 of the vignette). The multiplication results are the kernel argument settings, among which you want to search for the optimal one using cross-validation. |

`subset` |
If a subset of samples is to be used, give vector of column- indices of these samples in the original matrix here. |

`newlabels` |
If other labels than the ones in the MACAT-list-structure are to be used, give them as character vector/factor here. Make sure argument 'class' is one of them. |

`ncross` |
Integer. Specify how many folds in cross-validation. |

`verbose` |
Logical. Should progress be reported to STDOUT? |

A list of class 'MACATevP' with 4 components:

`[parameterName]` |
List of assessed settings for the parameter [parameterName]. |

`avgResid` |
Average Residual Sum of Squares for the parameter settings in the same order as the first component. |

`multiplier` |
Multiplier of the original parameters in the same order as the first components. |

`best` |
List of parameter settings considered optimal by cross- validation. Can be directly inserted under the argument 'kernelparams' of the 'evalScoring' function. |

MACAT development team

1 2 3 4 5 | ```
data(stjd)
evalkNN6 <- evaluateParameters(stjd, class="T", chromosome=6,kernel=kNN,
paramMultipliers=c(0.01,seq(0.2,2.0,0.2),2.5))
if (interactive()&&capabilities("X11"))
plot(evalkNN6)
``` |

macat documentation built on Nov. 1, 2018, 2:34 a.m.

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.