karlin: Karlin [p-value] [iid]

In localScore: Package for Sequence Analysis by Local Score

Karlin [p-value] [iid]

Description

Calculates an approximated p-value of a given local score value and a long sequence length in the identically and independantly distributed model for the sequence. See also mcc() function for another approximated method in the i.i.d. model

Usage

karlin(
  localScore,
  sequence_length,
  score_probabilities,
  sequence_min,
  sequence_max
)

Arguments

localScore	the observed local score
sequence_length	length of the sequence (at least several hundreds)
score_probabilities	the probabilities for each unique score from lowest to greatest
sequence_min	minimum score
sequence_max	maximum score

Details

This method works the better the longer the sequence is. Important note : the calculus of the parameter of the distribution uses the resolution of a polynome which is a function of the score distribution, of order max(score)-min(score). There exists only empirical methods to solve a polynome of order greater that 5 with no warranty of reliable solution. The found roots are checked internally to the function and an error message is throw in case of inconsistent. In such case, you could try to change your score scheme (in case of discretization) or use the function karlinMonteCarlo .

Value

A double representing the probability of a localScore as high as the one given as argument

Examples

karlin(150, 10000, c(0.08, 0.32, 0.08, 0.00, 0.08, 0.00, 0.00, 0.08, 0.02, 0.32, 0.02), -5, 5)

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