Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/calculateThreshold.R

`calculateThreshold`

returns the proportion of prioritised genes from a random selection
for supplied threshold. Furthermore, this function also fits a loess curve to the estimated points.
This allows the calculation of a threshold for priortisation of genes.

1 2 3 4 5 6 7 8 9 10 11 12 |

`X` |
A matrix of gene expression values. |

`exclude` |
A vector of indices of genes to exclude. |

`index.ref` |
A vector of indices of reference genes used for prioritisation. |

`set.size` |
An integer giving the size of the set of genes that are to be prioritised. |

`Weights` |
A object of class |

`thresholds` |
A vector of thresholds; values should be in the range |

`anno` |
A dataframe or a matrix containing the annotation of arrays in |

`Factor` |
A character string corresponding to a column name of |

`cpus` |
An integer giving the number of cores that are supposed to be used. |

`parallel` |
A logical value indicating whether parallel comuting should be used. |

The proportion of prioritized random genes is estimated by drawing 1000 random sets of genes and calculating how many would be prioritised at every given threshold. A gene is is prioritised if at least one correlation with a known reference gene is above the given threshold.

`calculateThreshold`

returns an object of class `Threshold`

.
An object of class `Threshold`

is a `list`

with the following components:

`Prop.values`

A vector of the proportion of prioritized genes.`Thresholds`

A vector containing the values in`threshold`

.`loess.estimate`

An object of class`loess`

.

Saskia Freytag

1 2 3 4 5 6 7 | ```
Y<-simulateGEdata(500, 500, 10, 2, 5, g=NULL, Sigma.eps=0.1,
250, 100, intercept=FALSE, check.input=FALSE)
anno<-as.matrix(sample(1:4, dim(Y$Y)[1], replace=TRUE))
colnames(anno)<-"Factor"
weights<-findWeights(Y$Y, anno, "Factor")
calculateThreshold(Y$Y, exclude=seq(251,500,1), index.ref=seq_len(10),
Weights=weights, anno=anno, Factor="Factor")
``` |

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