monteCarlo {localScore} | R Documentation |
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)
[Package localScore version 1.0.11 Index]