Time-Course Gene Set Analysis

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Documentation for package ‘TcGSA’ version 0.12.10

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

TcGSA-package	Time-course Gene Set Analysis
chisqmix	Chi-Squared Mixtures Distribution
ClusteredTrends	Cluster the genes dynamics into different dominant trends.
clustTrend	Cluster the genes dynamics into different dominant trends.
data_simu_TcGSA	Simulated Data for TcGSA
dchisqmix	Chi-Squared Mixtures Distribution
design	Simulated Data for TcGSA
expr_1grp	Simulated Data for TcGSA
expr_2grp	Simulated Data for TcGSA
gmt_sim	Simulated Data for TcGSA
multtest.TcGSA	Computing the P-value of the Likelihood Ratios Applying a Multiple Testing Correction
pchisqmix	Chi-Squared Mixtures Distribution
plot.ClusteredTrends	Cluster the genes dynamics into different dominant trends.
plot.TcGSA	Plot a Gene Set Trends Heatmap.
plot1GS	Plotting a Specific Gene Set
plotFit.GS	Plotting function for exploring the fitness of the mixed modeling used in TcGSA
plotMultipleGS	Plotting Multiple Gene Sets in a single plot
plotPat.1GS	Plotting a Specific Gene Set Stratifying on Patients
plotPat.TcGSA	Plot a Gene Set Trends Heatmap for each Patient.
plotSelect.GS	Plotting (several) Selected Gene Set(s) in some Subjects
print.ClusteredTrends	Cluster the genes dynamics into different dominant trends.
print.summary.TcGSA	Summarizing TcGSA
print.TcGSA	Computing the Likelihood Ratios for the Gene Sets under Scrutiny
print.TcGSA.LR	Computing the Likelihood Ratios for the Gene Sets under Scrutiny
qchisqmix	Chi-Squared Mixtures Distribution
rchisqmix	Chi-Squared Mixtures Distribution
signifLRT.TcGSA	Identifying the Significant Gene Sets
summary.TcGSA	Summarizing TcGSA
TcGSA	Time-course Gene Set Analysis
TcGSA.LR	Computing the Likelihood Ratios for the Gene Sets under Scrutiny
TcGSA.LR.parallel	Parallel computing the Likelihood Ratios for the Gene Sets under Scrutiny