perm_res: Pre-computed permutation results for simulated data...

In RC-88/CaDrA: Candidate Driver Analysis

Pre-computed permutation results for simulated data (sim_FS)

Description

The permutation result returned from CaDrA() using pre-simulated dataset (FS = sim_FS), pre-simulated input scores (input_score = sim_Scores), top_N = 7, method = "ks_pval", alternative = "less", search_method = "both", max_size = 10, obs_best_score = NULL and n_perm = 1000 as inputs to the function.

Usage

data(perm_res)

Format

A list of objects returned from CaDrA() function. The resulting object contains a list of key parameters that was used to run the permutation-based testing, a vector of permuted best scores for a given n_perm, an observed best score, and a permuted p-value.

To visualize the Empirical Null Distribution of the permuted best scores over n_perm iterations, just pass the resulting list to permutation_plot().

See permutation_plot() for more details.

References

Kartha VK, Kern JG, Sebastiani P, Zhang L, Varelas X, Monti S (2017) CaDrA: A computational framework for performing candidate driver analyses using binary genomic features. (Frontiers in Genetics)

Examples

# Load the pre-computed permutation results for sim_FS
data(perm_res)

# Plot the Empirical Null Distribution of the permuted best scores
# against its observed best score
permutation_plot(perm_res = perm_res)

RC-88/CaDrA documentation built on March 28, 2023, 12:18 a.m.