DaMiR.FSort {DaMiRseq} | R Documentation

## Order features by importance, using RReliefF filter

### Description

This function implements a procedure in order to rank features by their importance evaluated by RReliefF score.

### Usage

    DaMiR.FSort(data, df, fSample = 1)

### Arguments

`data` | A transposed data frame of expression data, i.e. transformed counts by vst or rlog. A log2 transformed expression matrix is also accepted. Rows and Cols should be, respectively, observations and features
`df` | A data frame with class and known variables; at least one column with 'class' label must be included
`fSample` | Fraction of sample to be used for the implementation of RReliefF algorithm; default is 1

### Details

This function is very time-consuming when the number of features is high. We observed there is a quadratic relationship between execution time and the number of features. Thus, we have also implemented a formula which allows the users to estimate the time to perform this step, given the number of features. The formula is:

T = 0.0011 * N^2 - 0.1822 * N + 27.092

where T = Time and N = Number of genes. We strongly suggest to filter out non informative features before performing this step.

### Value

A data frame with two culmuns, where features are sorted by importance scores:

- RReliefF score - Calculated by `relief` function, implemented in `FSelector` package;

- scaled.RReliefF score - Z-score value, computed for each RReliefF score.

A plot with the first 50 features ordered by their importance.

### Author(s)

Mattia Chiesa, Luca Piacentini

### References

Marko Robnik-Sikonja, Igor Kononenko: An adaptation of Relief for attribute estimation in regression. In: Fourteenth International Conference on Machine Learning, 296-304, 1997

### See Also

`relief`, `DaMiR.FSelect`, `DaMiR.FReduct`

### Examples

    # use example data:
    data(data_reduced)
    data(df)
    # rank features by importance:
    df.importance <- DaMiR.FSort(data_reduced[,1:10],
     df, fSample = 0.75)

[Package DaMiRseq version 2.0.0 Index]