View source: R/proposed_steps.R

select_ideal_k | R Documentation |

This function detects the optimal number of transcription factors which are regulating each target gene. This number is different for different target genes. It utilizes a heuristic to also detect the isolated targets which are not regulated by any transcription factor. To the detect the optimal number of Tfs for each target gene, it uses a notion similar to that used for optimization of the L-curve criterion for Tikonov regularization by evaluating the variable importance curve for each target gene.

select_ideal_k(experimentid, mink, filepath, imagepath, adjacency_matrix_path)

`experimentid` |
The id of the experiment being conducted. It takes natural numbers like 1,2,3 etc. By default it's 1. |

`mink` |
User specified threshold i.e. the minimum number of Tfs to be considered while optimizing the L-curve criterion. By default it's 0. |

`filepath` |
Path where some intermediate files will be written and provided by the function |

`imagepath` |
Path where an image of the variable importance curves for first 16 target genes will be written and provided by the function |

`adjacency_matrix_path` |
Path where an intermediate adjacency matrix will be written and provided by the function |

Returns a vector where each element represents the optimal number of transcription factors for each target gene.

Raghvendra Mall <rmall@hbku.edu.qa>

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