vim.norm {logicFS}R Documentation

Standardized and Permutation Based Importance Measure

Description

Computes a standarized or a permutation based version of either the Single or the Multiple Tree Measure.

Usage

vim.norm(object, mu = 0)

vim.perm(object, mu = 0, n.perm = 10000, n.subset = 1000, 
  adjust = "bonferroni", rand = NA)

Arguments

object either the output of logicFS or vim.logicFS with addMatImp = TRUE, or the output of logic.bagging with importance = TRUE and addMatImp = TRUE
mu a non-negative numeric value. Default is zero. However, mu should actually be set to a value larger than zero. See Details
n.perm the number of (sign) permutations used in vim.perm
n.subset an integer specifying how many permutations should be considered at once
adjust character vector naming the method with which the raw permutation based p-values are adjusted for multiplicity. If "qvalue", the function qvalue.cal from the package siggenes is used to compute q-values. Otherwise, p.adjust is used to adjust for multiple comparisons. See p.adjust for all other possible specifications of adjust. If "none", the raw p-values will be used. For more details, see Details
rand an integer for setting the random number generator in a reproducible case

Details

In both vim.norm and vim.perm, an one-sample t-statistic is computed for each prime implicant, where the numerator is given by VIM - mu with VIM being the single or the multiple tree importance, and the denominator is computed by B^-0.5 of the sample standard deviations of the B improvements of the considered prime implicant in the B logic regression models. (Note that VIM is computed by the mean over these B improvements.)

As using mu = 0 might lead to calling a prime implicant important even though it actually shows only improvements of 1 or even 0, mu should be set to a value larger than zero. A rule of thumb might be to set mu to about one third of diff, where a prime implicant should explain, i.e. be true for, at least diff more cases than controls to be considered as important.

In vim.norm, the value of this this t-statistic is returned as the standardized importance of a prime implicant. The larger this value, the more important is the prime implicant. (This applies to all importance measures – at least for those contained in this package.) Assuming normality, a possible threshold for a prime implicant to be considered as important is the 1-0.05/m quantile of the t-distribution with B-1 degrees of freedom, where m is the number of prime implicants.

In vim.perm, the sign permutation is used to determine n.perm permuted values of the one-sample t-statistic, and to compute the raw p-values for each of the prime implicants. Afterwards, these p-values are adjusted for multiple comparisons using the method specified by adjust. The permutation based importance of a prime implicant is then given by 1- these adjusted p-values. Here, a possible threshold for calling a prime implicant important is 0.95.

Value

An object of class logicFS containing

primes the prime implicants
vim the respective importance of the prime implicants
prop NULL
type the type of model (1: classification, 3: logistic regression)
param further parameters (if addInfo = TRUE)
mat.imp NULL
measure the name of the used importance measure
threshold the threshold suggested in Details
mu mu

Author(s)

Holger Schwender, holger.schwender@udo.edu

References

Schwender, H. (2007). Statistical Analysis of Genotype and Gene Expression Data. Dissertation, Department of Statistics, University of Dortmund, Dortmund, Germany.

See Also

logic.bagging, logicFS, vim.logicFS, vim.chisq, vim.ebam


[Package logicFS version 1.8.0 Index]