Description Usage Arguments Details Value Author(s) Examples

Perform feature selection or dimension reduction to remove noise variables.

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`data` |
data matrix with rows as samples and columns as variables |

`scale` |
logical; should the data be centered and scaled? |

`type` |
if we use "conventional" measures (default), then the mean and standard deviation are used for centering and scaling, respectively. If "robust" measures are specified, the median and median absolute deviation (MAD) are used. Alternatively, we can apply "tsne" for dimension reduction. |

`min.var` |
minimum variability measure threshold used to filter the
feature space for only highly variable features. Only features with a
minimum variability measure across all samples greater than |

We can apply a basic filtering method of feature selection that removes variables with low signal and (optionally) scales before consensus clustering. Or, we can use t-SNE dimension reduction to transform the data to just two variables. This lower-dimensional embedding allows algorithms such as hierarchical clustering to achieve greater performance.

dataset prepared for usage in `consensus_cluster`

Derek Chiu

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diceR documentation built on June 11, 2018, 5:04 p.m.

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