This package is a gene set analysis function for onesided test (OLS), twosided test (multivariate analysis of variance). If the experimental conditions are equal to 2, the pvalue for Hotelling's t^2 test is calculated. If the experimental conditions are great than 2, the pvalue for Wilks' Lambda is determined and posthoc test is reported too. Three multiple comparison procedures, Dunnett, Tukey, and sequential pairwise comparison, are implemented. The program computes the pvalues and FDR (false discovery rate) qvalues for all gene sets. The pvalues for individual genes in a significant gene set are also listed. MAVTgsa generates two visualization output: a pvalue plot of gene sets (GSA plot) and a GSTplot of the empirical distribution function of the ranked test statistics of a given gene set. A Random Forestsbased procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes.
Package details 


Author  ChihYi Chien, ChenAn Tsai, ChingWei Chang, and James J. Chen 
Maintainer  ChihYi Chien <92354503@nccu.edu.tw> 
License  GPL2 
Version  1.3 
Package repository  View on CRAN 
Installation 
Install the latest version of this package by entering the following in R:

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