Title: Compute and Visualize Bivariate Associations
Authors@R: person("Vonn", "Walter", email = "vwalter1@hmc.psu.edu", role = c("aut", "cre"))
Description: Pearson correlation coefficients are commonly used to quantify the strength
of bivariate associations of genomic variables.  For example, correlations of gene-level
DNA copy number and gene expression measurements may be used to assess the impact of
DNA copy number changes on gene expression in tumor tissue.  MVisAGe enables users to
quickly compute and visualize the correlations in order to assess the effect of regional
genomic events such as changes in DNA copy number or DNA methylation level.

Authors@R: person("Vonn", "Walter", email = "vwalter1@pennstatehealth.psu.edu", role = c("aut", "cre"))
Description: Pearson and Spearman correlation coefficients are commonly used to quantify the strength

DNA copy number changes on gene expression in tumor tissue.  'MVisAGe' enables users to
genomic events such as changes in DNA copy number or DNA methylation level.  Please see
Walter V, Du Y, Danilova L, Hayward MC, Hayes DN, 2018. Cancer Research

Title: Give power for a given effect size using multivariate
Depends: R (>= 2.7.1), randomForest, pamr, kernlab, class
Description: Calculate power for a given effect size and sample size
using multivariate classification methods: Random forest (RF),
Prediction analysis of microarrays (PAM), K-nearest neighbor
Packaged: Mon Feb 15 21:48:43 2010; yguo

Packaged: Fri Jul 30 18:55:48 2010; yguo

Title: Penalized Moving-Window Lasso Method for Genome-Wide Association
Description: The Moving-Window Lasso (MWLasso) method for genome-wide association studies. A window scans the design matrix. For predictors in the same window, their coefficients estimates are smoothed.

Title: Two Stage Moving-Window Ridge Method for Prediction and
Description: A two stage moving-window Ridge method for coefficients estimation and model prediction. In the first stage, moving-window penalty and L1 penalty are applied. In the second stage, ridge regression is applied.