get_shannon_diversity_index {sigminer} | R Documentation |
Get Shannon Diversity Index for Signatures
Description
H = - \sum_{i=1}^n{p_i ln(p_i)}
where n
is the number
of signatures identified in the signature with exposure > cutoff
,
and pi
is the normalized exposure of the ith signature with
exposure > cutoff
. Exposures of signatures were normalized to
sum to 1
.
Usage
get_shannon_diversity_index(rel_expo, cutoff = 0.001)
Arguments
rel_expo |
a |
cutoff |
a relative exposure cutoff for filtering signatures,
default is |
Value
a data.frame
References
Steele, Christopher D., et al. "Undifferentiated sarcomas develop through distinct evolutionary pathways." Cancer Cell 35.3 (2019): 441-456.
Examples
# Load mutational signature
load(system.file("extdata", "toy_mutational_signature.RData",
package = "sigminer", mustWork = TRUE
))
# Get signature exposure
rel_expo <- get_sig_exposure(sig2, type = "relative")
rel_expo
diversity_index <- get_shannon_diversity_index(rel_expo)
diversity_index
[Package sigminer version 2.3.1 Index]