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 3 4 5 6 7 8 9 10 | 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
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)
|
Warning message:
In file(con, "r") : cannot open file '/proc/stat': Permission denied
# A tibble: 500 x 3
gene importance pvalue
<chr> <dbl> <lgl>
1 Gene90 0.159 NA
2 Gene183 0.148 NA
3 Gene428 0.146 NA
4 Gene23 0.144 NA
5 Gene54 0.137 NA
6 Gene288 0.130 NA
7 Gene147 0.124 NA
8 Gene360 0.123 NA
9 Gene481 0.123 NA
10 Gene269 0.119 NA
# … with 490 more rows
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