Description Usage Arguments Value Examples

View source: R/gene_importances.R

Calculates the feature importance of each column in `x`

in trying to predict the time ordering.

1 2 | ```
gene_importances(x, time, num_permutations = 0, ntree = 10000,
ntree_perm = ntree/10, mtry = ncol(x) * 0.01, num_threads = 1, ...)
``` |

`x` |
A numeric matrix or a data frame with |

`time` |
A numeric vector containing the inferred time points of each sample along a trajectory as returned by |

`num_permutations` |
The number of permutations to test against for calculating the p-values (default: 0). |

`ntree` |
The number of trees to grow (default: 10000). |

`ntree_perm` |
The number of trees to grow for each of the permutations (default: ntree / 10). |

`mtry` |
The number of variables randomly samples at each split (default: 1% of features). |

`num_threads` |
Number of threads. Default is 1. |

`...` |
Extra parameters passed to |

a data frame containing the importance of each feature for the given time line

1 2 3 4 5 6 7 | ```
dataset <- generate_dataset(num_genes=500, num_samples=300, num_groups=4)
expression <- dataset$expression
group_name <- dataset$sample_info$group_name
space <- reduce_dimensionality(expression, ndim=2)
traj <- infer_trajectory(space)
# set ntree to at least 1000!
gene_importances(expression, traj$time, num_permutations = 0, ntree = 1000)
``` |

SCORPIUS documentation built on Aug. 7, 2019, 5:02 p.m.

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