FSmethod {HPiP} | R Documentation

## Feature Selection via Matrix Correlation and Recursive Feature Elimination (RFE)

### Description

This function performs feature selections via two approaches

- `filter.corr` - compute matrix correlation between features and filter using a threshold.

- `rfeFS` - perform recursive feature elimination (RFE) method wrapped with a Random Forest (RF) algorithm for feature importance evaluation.

### Usage

    FSmethod(
      x,
      type = c("cor", "rfe", "both"),
      cor.cutoff = 0.7,
      resampling.method = "cv",
      iter = 2,
      repeats = 3,
      metric = "Accuracy",
      verbose = TRUE
    )

### Arguments

`x` | A data.frame containing protein-protein interactions, class labels and features.
`type` | The feature selection type, one or two of `filter.corr` and `rfeFS`.
`cor.cutoff` | Correlation coefficient cutoff used for filtering. See `filter.corr` for more details.
`resampling.method` | The resampling method for RFE :'boot', 'boot632', optimism_boot',boot_all', 'cv', 'repeatedcv', 'LOOCV', 'LGOCV';defaults to cv. See `rfeFS` and `rfeControl` for more details.
`iter` | Number of partitions for cross-validation; defaults to 2. See `rfeFS` and `rfeControl` for more details.
`repeats` | For repeated k-fold cross validation only; defaults to 3.See `rfeFS` and `rfeControl` for more details.
`metric` | A string that specifies what summary metric will be used to select the optimal feature ; default to ROC.See `rfeFS` and `rfe` for more details.
`verbose` | Make the output verbose.See `rfeFS` and `rfeControl` for more details.

### Details

FSmethod

### Value

If the type set to `filter.corr` , the output includes the following elements:

- corProfile - A correlation matrix.

- corSelectedFeatures - Name of features that retained after the correlation analysis.

- cordf - A data.frame filtered.

If the type set to `rfeFS` , the output includes the following elements:

- rfProfile - A list of elements. See `rfe` for more details.

- rfSelectedFeatures - Name of features that retained in the feature selection process.

- rfdf - A data.frame filtered.

If type set to `both` the output includes the following elements:

- rfdf - The final data.frame that includes the selected features retained after both `filter.corr` and `rfeFS` analysis.

### Author(s)

Matineh Rahmatbakhsh, matinerb.94@gmail.com.

### Examples

    data('example_data')
    x <- na.omit(example_data)
    s <- FSmethod(x, type = 'both',
    cor.cutoff = 0.7, resampling.method = "repeatedcv",
    iter = 5, repeats = 3, metric = "ROC", verbose = TRUE)

[Package HPiP version 1.0.0 Index]