karlinMonteCarlo_double | R Documentation |

Estimates p-value, for integer scores, based on a Monte Carlo estimation of Gumble parameters from simulations of smaller sequences with same distribution. Appropriate for great sequences with length > 10^3, for i.i.d and markovian sequence models.

karlinMonteCarlo_double( local_score, sequence_length, simulated_sequence_length, FUN, ..., numSim = 1000, plot = TRUE )

`local_score` |
local score observed in a segment. |

`sequence_length` |
length of the sequence |

`simulated_sequence_length` |
length of simulated sequences produced by FUN |

`FUN` |
function to simulate similar sequences with. |

`...` |
parameters for FUN |

`numSim` |
number of sequences to create for estimation |

`plot` |
boolean value if to display plots for cumulated function and density |

The length of the simulated sequences is an argument specific to the function provided for simulation. Thus, it has to be provided also in the parameter simulated_sequence_length in the arguments of the "Monte Carlo - Karlin" function. It is a crucial detail as it influences precision and computation time of the result. Note that to get an appropriate estimation, the given average score must be non-positive.

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

new = sample(-7:6, replace = TRUE, size = 1000) #MonteCarlo taking random sample from the input sequence itself karlinMonteCarlo_double(local_score = 66, sequence_length = 1000, FUN = function(x, simulated_sequence_length) {return(sample(x = x, size = simulated_sequence_length, replace = TRUE))}, x=new, simulated_sequence_length = 1000, numSim = 1000) #Markovian example (longer computation) MyTransMat_reels <- 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, 0.3,0.3,0.1,0.2,0.1, 0.2,0.1,0.2,0.4,0.1),ncol = 5, byrow=TRUE) karlinMonteCarlo(local_score = 10.5,sequence_length=200,FUN = transmatrix2sequence, matrix = MyTransMat_reels, score =c(-1,-0.5,0,0.5,1),length=1500, plot=FALSE, numSim = 1500, simulated_sequence_length =1500)

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.