Package: GlobalAncova
Title: Global test for groups of variables via model comparisons
Version: 4.28.0
Date: 2021-01-27
Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with
        contributions from S. Knueppel
Description: The association between a variable of interest (e.g. two
        groups) and the global pattern of a group of variables (e.g. a
        gene set) is tested via a global F-test. We give the following
        arguments in support of the GlobalAncova approach: After
        appropriate normalisation, gene-expression-data appear rather
        symmetrical and outliers are no real problem, so least squares
        should be rather robust. ANCOVA with interaction yields
        saturated data modelling e.g. different means per group and
        gene. Covariate adjustment can help to correct for possible
        selection bias. Variance homogeneity and uncorrelated residuals
        cannot be expected. Application of ordinary least squares gives
        unbiased, but no longer optimal estimates
        (Gauss-Markov-Aitken). Therefore, using the classical F-test is
        inappropriate, due to correlation. The test statistic however
        mirrors deviations from the null hypothesis. In combination
        with a permutation approach, empirical significance levels can
        be approximated. Alternatively, an approximation yields
        asymptotic p-values. The framework is generalized to groups of
        categorical variables or even mixed data by a likelihood ratio
        approach. Closed and hierarchical testing procedures are
        supported. This work was supported by the NGFN grant 01 GR
        0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.
Maintainer: Manuela Hummel <manuela.hummel@web.de>
Depends: methods, corpcor, globaltest
Imports: annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
Suggests: GO.db, golubEsets, hu6800.db, vsn, Rgraphviz
License: GPL (>= 2)
biocViews: Microarray, OneChannel, DifferentialExpression, Pathways,
        Regression
Config/pak/sysreqs: libpng-dev libxml2-dev libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 13:57:03 UTC
RemoteUrl: https://github.com/bioc/GlobalAncova
RemoteRef: RELEASE_3_22
RemoteSha: 99efd2a3de5b97e7f6884f794a874fa94c0e717b
NeedsCompilation: yes
Packaged: 2025-11-11 19:33:48 UTC; root
Built: R 4.5.2; x86_64-w64-mingw32; 2025-11-11 19:41:01 UTC; windows
Archs: x64
