MAVTgsa: Three methods to identify differentially expressed gene sets, ordinary least square test, Multivariate Analysis Of Variance test with n contrasts and Random forest.

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

Author
Chih-Yi Chien, Chen-An Tsai, Ching-Wei Chang, and James J. Chen
Date of publication
2014-07-02 13:48:35
Maintainer
Chih-Yi Chien <92354503@nccu.edu.tw>
License
GPL-2
Version
1.3

View on CRAN

Man pages

data
Example data for MAVTn
design.matrix
Design matrix
GS
Example data for MAVTn
GSTplot
GST plot
Hott2
Hottelling's T square
ma.estimate
Estimate of the coefficients
MAVTgsa-package
OLS and Multivariate Analysis of Variance test for gene set...
MAVTn
OLS, Hottelling's T2 and MANOVA with n contrasts
MAVTp
Random Forests-based procedure
minp
P-values adjustment in permutation
Tols
Ordinary Least Square test
Wilksn
Wilk's Lambda for n-group multiple comparisons

Files in this package

MAVTgsa
MAVTgsa/NAMESPACE
MAVTgsa/data
MAVTgsa/data/GS.rda
MAVTgsa/data/data.rda
MAVTgsa/R
MAVTgsa/R/MAVTgsa.R
MAVTgsa/MD5
MAVTgsa/DESCRIPTION
MAVTgsa/man
MAVTgsa/man/GSTplot.Rd
MAVTgsa/man/MAVTgsa-package.Rd
MAVTgsa/man/MAVTn.Rd
MAVTgsa/man/Tols.Rd
MAVTgsa/man/Wilksn.Rd
MAVTgsa/man/MAVTp.Rd
MAVTgsa/man/data.Rd
MAVTgsa/man/minp.Rd
MAVTgsa/man/design.matrix.Rd
MAVTgsa/man/Hott2.Rd
MAVTgsa/man/ma.estimate.Rd
MAVTgsa/man/GS.Rd