View source: R/gene_importances.R
gene_importances | R Documentation |
Calculates the feature importance of each column in x
in trying to predict the time ordering.
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 M rows (one per sample) and P columns (one per feature). |
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
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.