monteCarlo: Monte Carlo method [p-value]

In localScore: Package for Sequence Analysis by Local Score

Monte Carlo method [p-value]

Description

Calculates an empirical p-value based on simulations of similar integer sequences of the same length. Perfect for small sequences (both markov chains and identically and independantly distributed) with length ~ 10^3. See function monteCarlo_double() for possible real scores.

Usage

monteCarlo(local_score, FUN, ..., plot = TRUE, numSim = 1000)

Arguments

local_score	local score observed in a segment.
FUN	function to simulate similar sequences with.
...	parameters for FUN
plot	boolean value if to display plots for cumulated function and density
numSim	number of sequences to generate during simulation

Value

Floating value corresponding to the probability to obtain a local score with value greater or equal to the parameter

Examples

monteCarlo(120, FUN = rbinom, n = 100, size = 5, prob=0.2)

new = sample(-7:6, replace = TRUE, size = 1000)
#MonteCarlo taking random sample from the input sequence itself

monteCarlo(local_score = 20, FUN = function(x) {return(sample(x = x, 
size = length(x), replace = TRUE))}, x=new)

# Markovian example
MyTransMat <-
+     matrix(c(0.3,0.1,0.1,0.1,0.4, 0.2,0.2,0.1,0.2,0.3, 0.3,0.4,0.1,0.1,0.1, 0.3,0.3,0.1,0.0,0.3,
+              0.1,0.1,0.2,0.3,0.3), ncol = 5, byrow=TRUE)

monteCarlo(local_score = 50,
          FUN = transmatrix2sequence, matrix = MyTransMat,
          length=150, score = c(-2,-1,0,2,3), plot=FALSE, numSim = 5000)

localScore documentation built on Nov. 3, 2023, 1:08 a.m.