vim.set {logicFS}R Documentation

VIM for SNPs and Sets of Variables

Description

Quantifies the importances of SNPs or sets of variables, respectively, contained in a logic bagging model.

Usage

  vim.snp(object, useN = NULL, iter = NULL, standardize = NULL, 
     mu = 0, addMatImp = FALSE, prob.case = 0.5, rand = NA)

  vim.set(object, set = NULL, useN = NULL, iter = NULL, standardize = NULL, 
     mu = 0, addMatImp = FALSE, prob.case = 0.5, rand = NA)

Arguments

object

an object of class logicBagg, i.e.\ the output of logic.bagging.

set

either a list or a character or numeric vector.

If NULL (default), then it will be assumed that data, i.e.\ the data set used in the application of logic.bagging, has been generated using make.snp.dummy or similar functions for coding variables by binary variables, i.e.\ with a function that splits a variable, say SNPx, into the dummy variables SNPx.1, SNPx.2, ... (where the “." can also be any other sign, e.g., an underscore).

If a character or a numeric vector, then the length of set must be equal to the number of variables used in object, i.e.\ the number of columns of data in the logicBagg object, and must specify the set to which a variable belongs either by an integer between 1 and the number of sets, or by a set name. If a variable should not be included in any of the sets, set the corresponding entry of set to NA. Using this specification of set it is not possible to assign a variable to more than one sets. For such a case, set set to a list (as follows).

If set is a list, then each object in this list represents a set of variables. Therefore, each object must be either a character or a numeric vector specifying either the names of the variables that belongs to the respective set or the columns of data that contains these variables. If names(set) is NULL, generic names will be employed as names for the sets. Otherwise, names(set) are used.

useN

logical specifying if the number of correctly classified out-of-bag observations should be used in the computation of the importance measure. If FALSE, the proportion of correctly classified oob observations is used instead. If NULL (default), then the specification of useN in object is used.

iter

integer specifying the number of times the values of the variables in the respective set are permuted in the computation of the importance of this set. If NULL (default), the values of the variables are not permuted, but all variables belonging to the set are removed from the model

standardize

should a standardized version of the importance measure for a set of variables be returned? By default, standardize = TRUE is used in the classification and the (multinomial) logistic regression case, and standarize is set to FALSE in the linear regression case. For details, see mu.

mu

a non-negative numeric value. Ignored if standardize = FALSE. Otherwise, a t-statistic for testing the null hypothesis that the importance of the respective set is equal to mu is computed.

addMatImp

should the matrix containing the improvements due to each of the sets in each of the logic regression models be added to the output?

prob.case

a numeric value between 0 and 1. If the logistic regression approach of logic regression has been used in logic.bagging, then an observation will be classified as a case (or more exactly, as 1), if the class probability of this observation is larger than prob.case. Otherwise, prob.case is ignored.

rand

an integer for setting the random number generator in a reproducible state.

Value

An object of class logicFS containing

vim

the importances of the sets of variables,

prop

NULL,

primes

the names of the sets of variables,

type

the type of model (1: classification, 2:linear regression, 3: logistic regression),

param

further parameters (if addInfo = TRUE in the previous call of logic.bagging), or NULL (otherwise),

mat.imp

either a matrix containing the improvements due to the sets of variables for each of the models (if addMatImp = TRUE), or NULL (if addMatImp = FALSE),

measure

the name of the used importance measure,

threshold

NULL if standardize = FALSE, otherwise the 1-0.05/m quantile of the t-distribution with B-1 degrees of freedom, where m is the number of sets and B is the number of logic regression models composing object,

mu

mu (if standardize = TRUE), or NULL (otherwise),

iter

iter.

Author(s)

Holger Schwender, holger.schwender@udo.edu

References

Schwender, H., Ruczinski, I., Ickstadt, K. (2011). Testing SNPs and Sets of SNPs for Importance in Association Studies. Biostatistics, 12, 18-32.

See Also

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


[Package logicFS version 1.50.0 Index]