quality: quality

Description Usage Arguments Author(s)

View source: R/BeeMarkov.R

Description

Compute the quality of the model and return a TRUE Positive or FALSE Negative information. It test the positive and negative model and assign every sequence of the fasta file to one model or the other. Therefore, the file must countain sequences which are know to be from one model.

Usage

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quality(file, pos_training = NULL, neg_training = NULL,
  trans_pos = NULL, trans_neg = NULL, l_word_pos = 1,
  l_word_neg = 1, n_train = 1, n_seq = 1, quiet = FALSE)

Arguments

file

a file (fasta) to read and use to test model

pos_training

a file (fasta) to read and train the positive model

neg_training

a file (fasta) to read and train the negative model

trans_pos

a transition matrix if it was already computed. Therefore, no need to train models. Warning, it must be in log

trans_neg

a transition matrix if it was already computed. Therefore, no need to train models. Warning, it must be in log

l_word_pos

length of words for the model. Equal to the "order of the model + 1"

l_word_neg

length of words for the model. Equal to the "order of the model + 1"

n_train

number of sequences to train with

n_seq

number of sequences to analyse

quiet

if some informations are print or not (boolean)

Author(s)

Jaunatre Maxime <maxime.jaunatre@etu.univ-grenoble-alpes.fr>


gowachin/BeeMarkov documentation built on Dec. 1, 2019, 2:57 a.m.