simulation: Simulation Analysis

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Simulation Analysis

Description

• simulate_signature() - Simulate signatures from signature pool.

• simulate_catalogue() - Simulate catalogs from signature/catalog pool.

• simulate_catalogue_matrix() - Simulate a bootstrapped catalog matrix.

Usage

simulate_signature(x, weights = NULL)

simulate_catalogue(x, n, weights = NULL)

simulate_catalogue_matrix(x)

Arguments

x	a numeric vector representing a signature/catalog or matrix with rows representing signatures/samples and columns representing components.
weights	a numeric vector for weights.
n	an integer indicating mutation number to be generated in a catalog.

Value

a matrix.

Examples

# Generate a catalog
set.seed(1234)
catalog <- as.integer(table(sample(1:96, 1000, replace = TRUE)))
names(catalog) <- paste0("comp", 1:96)
# Generate a signature
sig <- catalog / sum(catalog)

# Simulate catalogs
x1 <- simulate_catalogue(catalog, 10) # 10 mutations
x1
x2 <- simulate_catalogue(catalog, 100) # 100 mutations
x2
x3 <- simulate_catalogue(catalog, 1000) # 1000 mutations
x3
# Similar with a signature
x4 <- simulate_catalogue(sig, 10) # 10 mutations
x4

# Load SBS signature
load(system.file("extdata", "toy_mutational_signature.RData",
  package = "sigminer", mustWork = TRUE
))
s <- t(sig2$Signature.norm)
# Generate a signature from multiple signatures/catalogs
s1 <- simulate_signature(s)
s1
s2 <- simulate_signature(s, weights = 1:3)
s2
# Generate a catalog from multiple signatures/catalogs
c1 <- simulate_catalogue(s, 100, weights = 1:3)
c1

sigminer documentation built on May 29, 2024, 3:11 a.m.